Yes, the whole app will be Linux Mobile ready soonish, but priority was to have the main screen first and get everything ready in-time for Debian stable inclusion
I wouldn't call it a fundamental difference. If I was to concatenate the 3 XMPP RFCs and the suggested XEPs from the compliance suite linked, I would end up with a monolithic spec.
Every now and then, when a new compliance suite is published, I'd need to update the one concatenated document aka. monolithic spec. A new compliance suite in XMPP "activating" a XEP is like "merging" an MSC. For as long as a XEP is not part of the compliance suite, it's not part of the monolithic spec (it's still just an MSC) and you don't have to mess with it.
The only real difference is that the current version of XMPP spec is a document with links to other documents whereas the current version of Matrix spec is a document with links inside the document itself.