Even if the two components are assembled separately then joined, doesn't necessarily argue that they can separate at will and function independently. The whole point of the separation bit was to keep the families out of harm's way, but they seemed to have dropped the whole families on starships bit after Wolf 359 and definitely after the Dominion war. Rightly so.
Voyager never had any civilians on it when they launched. If they could separate the whole time, why was it not even mentioned once as an alternative at some point when Janeway was ready to blow up the ship on any number of occasions?