^With regard to Enterprise NX-01 not being on the legacy walls, we have two reasons for that logistically.
The first is obvious: Enterprise hadn't even been conceived when those legacy walls were built for TMP and TNG.
The second would be a little more ambiguous, but one that carries at least some weight -- NX-01 may have been the first starship Enterprise, but it was NOT the first Federation
If we are to go by events shown in "These Are The Voyages...," one can likely assume that NX-01 was in the process of being decommissioned (or entirely so; we don't really get much in the way of how much time passes between Trip's death and the conference) by the time Archer gives his big Federation koom-by-ya speech.
Personally, I don't mind the idea that the signal from 'Regeneration' later influences the events of 'Q-Who?' only because of what happened in First Contact.