A second filter would technically work but consider that the same restriction on the number of master slots available to a plugin also applies to your bashed patch. If the first filter exhausts that space, chances are the patch would also get exhausted and that just doesn't turn out well. So there's not going to be a case where we hog up all 255 master slots on our filter because then we'd be monopolizing the patch at the expense of other things that also need it, including our own modules that need patch support.
So while we do still have some wiggle room, I'd rather not burn that up by supporting individual cells like those inns. It makes more sense to support them all via a merged plugin.
Just for curiosity, what sort of compatibility issues are you facing that require the plugins to remain separated?
I think I understand a bit better about the limitations of the filter patch now, and that's good and sound thinking.
Vis-a-vis Cyrodiil Inns, it has been a while but as I recall the biggest trouble was with Merry Bell Inn and the quest mod Armageddon. Pine Peak Lodge also occupied what had/has become some crowded real estate. There are a number of patches for the Cloudtop area, but weird things kept popping up around there and something or other was fouling Weynon Retreat. I fiddled with my load order and managed to find a somewhat happy medium but that is with Merry Bell fairly early and Pine Peak fairly late, close to where BOSS assigns them. I have since subtracted a few things from my order so it might not be as much of an issue now, but after spending a good while trying things at the time I eventually just took those two out. The Cyrodiil Inns esp's were generally quite nice though - not overambitious, just simple additions that seemed to fit in well to the game world. I wasn't as much of a fan of Pine Peak as of the rest, but maybe that's because it gave me grief.
In any event, I totally agree that given the circumstances supporting them as a merged plugin is more than sufficient.