For messaging app I don't think it'd be a huge deal, I could see ROMs just shipping with something like Silence or some other open messaging app, since there's a lot of them. Dialer is the one I could see being an issue. I think what's most likely to happen is there's going to be a new go to open source dialer app specifically made for this purpose. It'd make more sense than every ROM making and maintaining their own dialer, except maybe the big ones like Lineage and Graphene.
I definitely agree that this will be an issue, especially as they do more and more stuff like this. This specific change I think will actually be better in the long-run. I find the community made apps for this sort of thing tend to be better than the default AOSP ones anyway.
For the long term though it says some negative things about Google and their intentions for AOSP, wonder what will happen as they retire more and more features of it. Maybe there will be an AOSP fork which is made to kind of replace AOSP, I could kind of see that happening. Something that aims to stay updated with the new code, but also tries to break away from as much dependencies as possible.
These are just some of my thoughts/theories.