yeah, its trivial to do in mother.pd. just [r fs], and convert it to [s aux] (basically)
you can choose to put mother.pd in either system or patch directory to decide if its for all patches or just one.
(because some patches may have explicit support for fs which you want to keep )
see releases/beta posts about this topic.
has to be done every time a patch is run, but that’ll happen anyway if your changes are in mother.pd
Note: the reason override mother.pd is not perfect (and we avoid) is when new releases are made , mother.pd may have been updated, for new functionality - having an old mother.pd (your copy) hanging around can break the functionality.
that said in 3.x, I introduced versioning, so what now happens is if the Organelle deems that you patch is ‘incompatible’ then it will move your mother.pd to one side (not delete it!) , and revert to the new mother.pd …
(it does warn about this, but you wont see the warning, you’ll just suddenly find your ‘extra’ functionality no longer works - and on inspection find your mother.pd renamed )