Interesting — RAPL is present, so thermald's "NO RAPL sysfs present" message is unexpected. It may be a permissions issue accessing the files inside, or a bug in the installed version of thermald.

It would be useful to see more of thermald's log:

journalctl -u thermald --no-pager | head -80

In the meantime, since thermald is clearly not managing thermals correctly and the i7-4790K has its own built-in thermal protection, disabling it is likely a safe option:

sudo systemctl disable --now thermald
echo "schedutil" | sudo tee /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor

If the CPU frequency is normal after this, that would confirm thermald was the cause.

$sudo journalctl -u thermald --no-pager | head -80
mag 26 20:19:37 ms7816 systemd[1]: Starting thermald.service...
mag 26 20:19:38 ms7816 thermald[5176]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 20:19:38 ms7816 thermald[5176]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 20:19:38 ms7816 thermald[5176]: Using config file /etc/thermald/thermal-conf.xml
mag 26 20:19:38 ms7816 thermald[5176]: Polling mode is enabled: 4
mag 26 20:19:38 ms7816 systemd[1]: Started thermald.service.
mag 26 21:38:58 ms7816 systemd[1]: Stopping thermald.service...
mag 26 21:38:58 ms7816 thermald[5176]: Terminating ...
mag 26 21:38:59 ms7816 thermald[5176]: terminating on user request ..
mag 26 21:39:00 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 26 21:39:00 ms7816 systemd[1]: Stopped thermald.service.
-- Boot e47ce3f9dccd46b9b18d9904e1a3badf --
mag 26 21:39:35 ms7816 systemd[1]: Starting thermald.service...
mag 26 21:39:35 ms7816 thermald[5098]: NO RAPL sysfs present
mag 26 21:39:35 ms7816 thermald[5098]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 21:39:35 ms7816 thermald[5098]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 21:39:35 ms7816 thermald[5098]: Using config file /etc/thermald/thermal-conf.xml
mag 26 21:39:35 ms7816 thermald[5098]: Polling mode is enabled: 4
mag 26 21:39:35 ms7816 systemd[1]: Started thermald.service.
mag 26 22:25:03 ms7816 systemd[1]: Stopping thermald.service...
mag 26 22:25:03 ms7816 thermald[5098]: Terminating ...
mag 26 22:25:04 ms7816 thermald[5098]: terminating on user request ..
mag 26 22:25:05 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 26 22:25:05 ms7816 systemd[1]: Stopped thermald.service.
-- Boot 3258e618cb914964a9fbf6125a131c9d --
mag 26 22:25:42 ms7816 systemd[1]: Starting thermald.service...
mag 26 22:25:43 ms7816 thermald[5117]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 22:25:43 ms7816 thermald[5117]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 22:25:43 ms7816 thermald[5117]: Using config file /etc/thermald/thermal-conf.xml
mag 26 22:25:43 ms7816 thermald[5117]: Polling mode is enabled: 4
mag 26 22:25:43 ms7816 systemd[1]: Started thermald.service.
mag 26 22:48:20 ms7816 systemd[1]: Stopping thermald.service...
mag 26 22:48:20 ms7816 thermald[5117]: Terminating ...
mag 26 22:48:21 ms7816 thermald[5117]: terminating on user request ..
mag 26 22:48:22 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 26 22:48:22 ms7816 systemd[1]: Stopped thermald.service.
-- Boot 06b3845c283d478fb146c9e590047bf4 --
mag 26 22:49:36 ms7816 systemd[1]: Starting thermald.service...
mag 26 22:49:36 ms7816 thermald[5068]: NO RAPL sysfs present
mag 26 22:49:36 ms7816 thermald[5068]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 22:49:36 ms7816 thermald[5068]: NO RAPL sysfs present
mag 26 22:49:36 ms7816 thermald[5068]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 26 22:49:36 ms7816 thermald[5068]: Using config file /etc/thermald/thermal-conf.xml
mag 26 22:49:37 ms7816 thermald[5068]: Polling mode is enabled: 4
mag 26 22:49:37 ms7816 systemd[1]: Started thermald.service.
mag 27 10:30:40 ms7816 thermald[5068]: Terminating ...
mag 27 10:30:40 ms7816 systemd[1]: Stopping thermald.service...
mag 27 10:30:41 ms7816 thermald[5068]: terminating on user request ..
mag 27 10:30:42 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 27 10:30:42 ms7816 systemd[1]: Stopped thermald.service.
-- Boot a9d80632af6a403bb89c1e67873c0fec --
mag 27 16:42:49 ms7816 systemd[1]: Starting thermald.service...
mag 27 16:42:49 ms7816 thermald[5014]: NO RAPL sysfs present
mag 27 16:42:49 ms7816 thermald[5014]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 27 16:42:49 ms7816 thermald[5014]: NO RAPL sysfs present
mag 27 16:42:49 ms7816 thermald[5014]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 27 16:42:49 ms7816 thermald[5014]: Using config file /etc/thermald/thermal-conf.xml
mag 27 16:42:49 ms7816 thermald[5014]: Polling mode is enabled: 4
mag 27 16:42:49 ms7816 systemd[1]: Started thermald.service.
mag 31 11:25:58 ms7816 systemd[1]: Stopping thermald.service...
mag 31 11:25:58 ms7816 thermald[5014]: Terminating ...
mag 31 11:25:59 ms7816 thermald[5014]: terminating on user request ..
mag 31 11:26:00 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 31 11:26:00 ms7816 systemd[1]: Stopped thermald.service.
-- Boot 55d42ef6be3b4e66ad022368c0fba8f4 --
mag 31 11:26:35 ms7816 systemd[1]: Starting thermald.service...
mag 31 11:26:35 ms7816 thermald[4773]: NO RAPL sysfs present
mag 31 11:26:35 ms7816 thermald[4773]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 31 11:26:35 ms7816 thermald[4773]: NO RAPL sysfs present
mag 31 11:26:35 ms7816 thermald[4773]: 13 CPUID levels; family:model:stepping 0x6:3c:3 (6:60:3)
mag 31 11:26:36 ms7816 thermald[4773]: Using config file /etc/thermald/thermal-conf.xml
mag 31 11:26:36 ms7816 thermald[4773]: Polling mode is enabled: 4
mag 31 11:26:36 ms7816 systemd[1]: Started thermald.service.
mag 31 16:18:54 ms7816 thermald[4773]: Terminating ...
mag 31 16:18:54 ms7816 systemd[1]: Stopping thermald.service...
mag 31 16:18:55 ms7816 thermald[4773]: terminating on user request ..
mag 31 16:18:56 ms7816 systemd[1]: thermald.service: Deactivated successfully.
mag 31 16:18:56 ms7816 systemd[1]: Stopped thermald.service.

I have applied these changes and rebooted, as suggested. The situation hasn't changed, maybe the cause is something else?

sudo systemctl disable --now thermald
echo "schedutil" | sudo tee /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor


grep . /sys/devices/system/cpu/cpu*/cpufreq/scaling_* 2>/dev/null | sed -n '1,40p' | grep scaling_cur_freq
/sys/devices/system/cpu/cpu0/cpufreq/scaling_cur_freq:800047
/sys/devices/system/cpu/cpu1/cpufreq/scaling_cur_freq:800056
/sys/devices/system/cpu/cpu2/cpufreq/scaling_cur_freq:800050
/sys/devices/system/cpu/cpu3/cpufreq/scaling_cur_freq:800027
/sys/devices/system/cpu/cpu4/cpufreq/scaling_cur_freq:800052
/sys/devices/system/cpu/cpu5/cpufreq/scaling_cur_freq:800040

Maybe the command was the issue.

$cat /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor
userspace
userspace
userspace
userspace
userspace
userspace
userspace
userspace

I believe this should have been changed to schedutil, is that right? This changes at reboot.
Without rebooting cpu frequency is as expected

$grep . /sys/devices/system/cpu/cpu*/cpufreq/scaling_* 2>/dev/null | sed -n '1,40p' | grep scaling_cur_freq
/sys/devices/system/cpu/cpu0/cpufreq/scaling_cur_freq:3165508
/sys/devices/system/cpu/cpu1/cpufreq/scaling_cur_freq:3197528
/sys/devices/system/cpu/cpu2/cpufreq/scaling_cur_freq:3197465
/sys/devices/system/cpu/cpu3/cpufreq/scaling_cur_freq:2782051
/sys/devices/system/cpu/cpu4/cpufreq/scaling_cur_freq:4260972
/sys/devices/system/cpu/cpu5/cpufreq/scaling_cur_freq:4221910

Therefore your suspicion was correct

The echo schedutil command at runtime restored normal frequency (3-4 GHz), which points to the userspace governor with 800 MHz as the cause. Since the governor still reverts to userspace after each reboot even with thermald disabled, it would be useful to check whether thermald is truly not running after the reboot:

systemctl status thermald

Also useful:

cat /sys/devices/system/cpu/intel_pstate/status

If thermald is stopped and disabled, the userspace governor being set at boot may be related to the intel_pstate driver mode. If the status is passive, the cpufreq framework is in use and something may be defaulting to userspace on this hardware.

$sudo systemctl status thermald
○ thermald.service - Thermal Daemon Service
Loaded: loaded (/usr/lib/systemd/system/thermald.service; disabled; preset: enabled)
Active: inactive (dead)
$cat /sys/devices/system/cpu/intel_pstate/status
passive

thermald is confirmed disabled and inactive, and intel_pstate is in passive mode (expected on Haswell without HWP support). The userspace governor being set at every boot may be related to the kernel default governor configuration, which is something that may need to be addressed at the distribution level.

As a test that should also resolve the issue, you can add cpufreq.default_governor=schedutil to the kernel command line. Edit /etc/default/grub and add it to GRUB_CMDLINE_LINUX, then run:

sudo update-grub

After the next reboot the CPU governor should default to schedutil instead of userspace, and the frequency should behave normally without any manual intervention.

From the distribution side, a kernel update is being prepared that sets schedutil as the default governor at boot, which should resolve the issue for all users without requiring any manual configuration.