Hey,
Do I understand correctly that you have pre-comped your whole character?
In which case my approach would be to set the character shapes fill as white, the strokes as black, and use a Luma track matte instead of an Alpha matte. Would that help?
A luma track respects alpha. The logic is that transparency is matted black, the same as your black strokes. Then the luma track matte maps all blacks to transparent.
Any stroke you don’t want to be transparent make white in the precomp.
Forgive my very rough recreation of your your character, but these screenshots should illustrate what I mean.


Hope this helps!