Thank you Miro, this helped indeed now!
We figured out that the E2 EDID we were working with has 10 bit color/channel per default.
We were having this problem with both LTSB 2016 with all the fixes installed - including this cumulative update - and lately with LTSC 2019.
LTSC 2019 seems to have changed the EDID management behavior - EDID from physical outputs may now override the AMD driver settings even with "Force EDID" checked, which is disturbing. Other than that it seems to run stable and has way less unnecessary programs and services pre-installed.
Yes, we are using 6.3.1
To compare with AMD 17q4.1 we are also testing the current 19q1.1 version - it seems like all start-up routines speed-up significantly including S400 sync settings after reboot.
Thank you again!