Mike Okuda himself has stated that registries are not always chronological. Mostly, yes, but not always. If you don't feel like accepting my examples, fine. But if you're going to ignore the guy who had been officially in charge of stuff like this for a long time, then that's your own issue.
Excelsiors with high registries vs. Ambassadors with low registries: I would thing that this would be obvious to you. A more advanced ship has a much lower registry than a lesser advanced one, implying that Starfleet decided to abandon the newer design in favor of rebuilding a much older one. That makes no sense to me.
It's stated that the Pegasus was a twelve year old ship. Not that it was a 30 year old ship with refits. Occam's Razor.
I know the Prometheus's reg was a VFX mistake. I was using it as an example of why the regs for the FC ships could also be a similar mistake as far as their build dates vs. their registries go.
ILM's VFX dept. vs. Mike Okuda: Yeah, it does kinda matter, because here you have a disconnect between the person making sure ships have correct registries, and a division of a company that might not have had the same information Okuda had.