I'm not a security expert, but my humble view is that if you need plugins for really basic functionality, that's a red flag.
I believe it is hard to get right, and only worthwhile on 1:1 communication, it doesn't work well at all on large chat rooms, which is what IRC is.
Regardless, if you don't want E2EE to be handled by a plugin- it is possible to make a client with it baked in.
There is no company that will stop you creating a third-party client unlike slack/discord which are extremely hostile to those endeavors by comparison.
EDIT: If you downvote without replying I'm just going to assume you're ideologically opposed to open standards, because I'm not sure what else I can take from it.
You can't downvote direct replies.
---
Speaking about standards; have you looked at IRCv3? Is there anything specific that you feel is not being addressed?
Encryption (to my mind) is better handled outside of the spec itself, just like HTTP vs TLS wrapped HTTP (HTTPS) where the "TLS" has no bearing at all on how HTTP is implemented.
IRCv3 is attempting to address the persistence issues, though many people like the lack of persistence in general.
I don't want to guess at what your concerns are, but more generally; have you looked at the spec?