While the test-run with the sub-microsecond estimation precision is running, I was reviewing the logs from the previous run:

... which was not too great considering some data loss and an unstable GPS readout.
Small side-note: actual pulse counter was working, but only the register readout had a too-small timeout value. This is a topic for another post, but with the reference clock being switched back- and forth, you also see the drift of the internal clock compared to the GPS.

But you also see periodic temperature drops, which made me wonder where they come from. Is some abrupt heating / cooling happening when I am not in the office?

But after watching the Video of CuriousMarc about the Display and remembering "Taking a lot of power"... It hit me.

Do you see it? I dim the display at nighttimes to reduce Eye-Strain and in that glass-dome the "dayBrightness" (5 of 7) actually heats up the thing! And to make matters worse, the heat rises up to the Temperature Sensor, but most of the Tuning Fork is actually below the display, making it worse to correlate measured temperature with actual tuning fork temperature.
So my first change will be to set it to "medium brightness" all the time to not throw the measurement off, and on the long run probably will drill a vent-hole into the Glass-Dome's top to allow the air to circulate (and / or put the temperature sensor on the bottom half).

Weird Problem to have; but when the PPMs count, this is actually measurable in the precision!

Here in the last image you see that the "Difference per period" (which is a measure of precision) is actually worse (most off-zero) when the system is non-uniformly heated by the display.