(I left a comment before reading some of the thread here, and it turns out my point was largely redundant)
I am also fairly annoyed with the way system is handled with flakes. But I’m also annoyed at how people have basically thrown overlays out the window because of the non-composable static outputs attrset. If I have to override a common dependency to add a patch or something, it’s now a rat’s nest of manual .override calls and praying that I didn’t miss anything. That, or I have to fork something and then I’m left with the same problem except with a rat’s nest of follows.
I know the output schema includes an attr for overlays, but it seems like no one ever uses it, and it’s also not clear whether a flake is expected to include its own inputs’ overlays in its output overlays, or if the consumer of the flake is expected to compose them. It’s a mess.
Personally, I think flakes really need solutions to these problems. But it doesn’t seem like that’s ever going to happen, so I guess they should just be released as-is 