TartaricAcid/TouhouLittleMaid#649
I unfortunately discovered that using Cloth Config API to change at least Touhou Little Maid's (possibly more affected) config via the in-game menu causes it to reset to the original state, be it stock or before having used CCA.

Uncertain of who's truly responsible for this unintended behavior I might as well created two bug reports on the matter.
If you require more information, don't hesitate to request such. Although based on what I provided on TartaricAcid's page should already suffice to easily replicate the issue in question.