Thanks for the good question, this has been fixed and will be available in the next update.
In any case, the STAB TRIM will always work when autopilot is enabled.

If this is critical for you right now, you can do the following:
- open the systems.cfg file
- find auto_throttle_hold_vs=1
- add the following lines after this line: 
pitch_use_trim = 0
pitch_use_elevator_only = 1

Please see #1 in the picture.

Also, two yellow switches LONG TRIM (#3) can be disabled by STABILIZER TRIM OFF button (#2).