If this helps then it could be considered to be configurable, similar to view->options->MIDI->reset all controllers on playback start,
maybe view->options->Audio->reset all audio tracks on playback start
EDIT:
I got audio clips out of sync when loop jumped to the start as well if the audio clip started before loop's start.
I noticed that the phasing is fixed while playing when all the audio tracks are selected and I mute and unmute them.
So I think it would be interesting to see if the following modification (maybe in another branch) will stabilize it:
Whenever the loop is acivated or deactivated OR the playhead is repositioned¹ then
for all audio tracks that are not muted
mute track and unmute track
1.) e̵x̵c̵e̵p̵t̵ ̵w̵h̵e̵n̵ ̵t̵h̵e̵ ̵r̵e̵p̵o̵s̵i̵t̵i̵o̵n̵i̵n̵g̵ ̵h̵a̵p̵p̵e̵n̵s̵ ̵b̵e̵c̵a̵u̵s̵e̵ ̵t̵h̵e̵ ̵p̵l̵a̵y̵h̵e̵a̵d̵ ̵r̵e̵a̵c̵h̵e̵s̵ ̵t̵h̵e̵ ̵l̵o̵o̵p̵'̵s̵ ̵e̵n̵d̵ ̵a̵n̵d̵ ̵j̵u̵m̵p̵s̵ ̵t̵o̵ ̵t̵h̵e̵ ̵l̵o̵o̵p̵'̵s̵ ̵s̵t̵a̵r̵t̵
If this helps then it could be considered to be configurable, similar to view->options->MIDI->reset all controllers on playback start,
maybe view->options->Audio->reset all audio tracks on playback start
EDIT:
I got audio clips out of sync when loop jumped to the start as well if the audio clip started before loop's start.