I tend to be in the same mind regarding registries, in that I generally don't infer the Jeffries system or any significant chronology from the numbers. If the registries are primarily batch sets, then they might not follow a specific sequencing.
I personally see no problem with some designs lasting decades or even a century or more, assuming they're efficient enough and Starfleet has more advanced technology than we currently do. However, I tend to be more conservative when it comes to doing a TOS version of a TMP or TNG era design. In some cases I think that's been done well (Mastercom's Coventry/Surya designs being TOS progenitors of the Miranda family), but I also think it becomes a bit silly to assume every basic design originated in a specific era and was then only periodically modified afterward.