Right. In-universe one way, chronologically goes the other way.
But it seems the NX as used for Excelsior is akin to current day military usage. XB-70 Valkyrie bomber is experimental, and in service it'd become B-70. And the Raptor was XF-22 experimental then YF-22 prototype then F-22 in service.
So NX-2000 would become NCC-2000 in service, as seen.
This fits with historical precedent and makes sense.
But if all that is untrue, NX did NOT indicate anything about an experimental vessel, as you suggest. Well why wouldn't it?
And if so, what's the meaning of NX as used on Enterprise?
NX class? Random letters-class?
In-universe, what I think got in the way of what should have been done is the 800-kb gorilla in the room - the Romulan War. This is the way that season 5, maybe season 6, should have gone. There is so much story-telling to be done within that very brutal, disruptive span of time. Think about what happens - Earth, Andor, Vulcan and Tellar end up being drawn together to face and defeat (we think) the Romulan threat, and in the span of 4-6 years, a group of disparate governments are thrown together into a new, tentative, umbrella government - The United Federation of Planets - which, canonically now, Jonathan Archer helped to facilitate.
I think the Earth Star Fleet can be forgiven for not following naming conventions during what was Earth's first wartime in space.