The only way/option to achieve the scope to have the custom object at file system level is to use both kind of objects ('XDO XML Publisher Template Files' setup obj at DB level and custom object).
In this way, you will have the object executed (Uploaded/downloaded) at DB level and copied at the filesystem.
This means you have to add to the CSR both objects.
If needed development might think to change the object type so that it also copies the file to the file system and supposed
to be copied to <PRODUCT_TOP>/patch/115/publisher directory. This is not yet implemented.