The way I see it, the EU probably doesn't really care if Apple keep ALL the restrictions they currently have on their App Store in actuality, as long as options exist on the platform.
So the solution to allowing access to NFC hardware will probably just be Apple opening up sideloading.
I personally hope that Apple implements sideloading in a way that allows those who don't want to use it to keep their device secure, and I'm confident they will.
Regarding the messaging platforms, I'm pretty sure the EU are not going to push us into a situation where E2E is broken, in fact, I was under the impression that the bills specifically required that E2E be maintained.