i would like to chime in to say my piece (since this was a thing i requested in the past on the github as well)
it has a lot of advantages, and from what i have heard, one of the reasons GNUSocial is liked is the multiple UI options (albeit all forcibly bundled with a UI if i understand correctly)
a better solution than this is to just straight up have some sort of setup wizard or installer, while i do not know how MUCH that would require, i could definitely imagine a command line tool at the very least that allows you to pick a UI to have bundled with the instance you are hosting.
i do not know how hard it will be to seperate them, nor how much the resources cost to host one of these user-side clients, but i can only see good coming of this seperation.
examples include: multi-account support being much easier to implement by seperating the two, and allowing a user to “try a UI” on an instance that hosts a seperate UI choice, via logging into their existing instance. this would allow someone to try the newer UI on a newer distribution of mastodon while keeping the same account, etc.
the only negative i have heard is the ones that gargron suggested. an argument i would have against this is to not seperate the github itself, and instead seperate into two subfolders, with an option somewhere to enable or disable the UI.
this would keep the same amount of effort to maintain it, while allowing all of the positives as far as i understand it.