Ultimately, if you can't find a solution, you can "de-modularize" the mod.
How to do that: take a copy of each of the 11 BtS XML files corresponding to the files that are in JARM\Assets\Modules\ChooseReligions. Skip the Schema files as they are not changed by JARM, just needed for modular loading.
Create in the JARM\Assets\XML folder the same sub-folder as in BtS: Art, Buildings, GameInfo, Technologies, Text, Units. Place there the 11 BtS XML files. With a text editor, insert after each last Tao Religion object the content of the respective JARM files.
All the art, you can leave it there in the "Modules" folder. If you put it elsewhere, you would just have to change all the paths in the ArtDefines files.
That's what I did a long time ago, as the basis of my own private mod.