at least Pleroma tries to take what Mastodon implemented and try to make it secure (through capability URIs), but still, don't use this for anything critical, at least not right now.
E2E encryption in fediverse context is very difficult to achieve: one actor, many devices.
would need to send separate subenvelopes to do OMEMO. very messy.
maybe it will happen some day, but we have to fix AP security first through properly defining best practices (litepub) before it's even worth discussing that.
AP XEP-like extension model is another security nightmare.
I think it is likely that litepub and AP will wind up evolving differently, but there will always be some level of compatibility...