Yes, i think that makes sense. Can't look at that pull request right now, but my current thinking is to leave the URI unprocessed if the scheme is anything other than file://.
Then file-name-handler-alist can decide what to do with it.
But warning the user on such occasions sounds a bit too noisy. Maybe a one-time warning.
The only other thing to watch out for is that wherever find-file lands is, its buffer-file-name should probably be left with the unchanged URI, so that eglot--path-to-uri can return it and tell the LSP server that we're now managing the buffer using the original URI.
João