No doubt that it's low priority right now. My guess is, considering how long this has remained ignored by Cryptic, it'll probably continue to stay ignored for a good while, at least until there's less on Cryptic's development schedule to allow this issue to be looked at.
I use an MVAM console, and it would be nice to have the sections match based on how we've customized our ship, in addition to keeping visuals from various equipment set pieces to stay on their respective sections.
The Prometheus class I have with my main, her main ship, is a mix and match of all four of those designs and her MVAM mode even indicates that - USS Shore-F MVAM Mode ~ http://reinahw.deviantart.com/#/d47qb0q
Althrough it looks like the bottom section reverts to the Prometheus design when reconnecting, odd.
While less of a noticeable thing: The Galaxy-R does this as well. I have mine customized as a Monarch class, but whenever I separate the saucer, all visuals cease; when the saucer returns, it is the Galaxy saucer until fully reconnected.
Too lazy to dig it up, but they've said at least once that this is simply a shortcoming of the technology. At the moment there's nothing they can do about it, but the possibility of the tech being improved upon later exists, so eventually this could be "fixed".