In TOS, the auxiliary control room is used for other things while the main bridge is still usable, apparently. In "And the Children Shall Lead," it seems to be used as an engineering operations center (unlike this being done in the engineering set most of the time), and in "The Way to Eden," it is specifically used for navigation while the bridge is navigating the ship. Other episodes show it manned while the bridge is doing something. Since the auxiliary control room is roughly the same idea as the Battle Bridge, it seems that it could be manned for something while the ship is not separated.
Perhaps navigation problems are its function during that time.
While I'm at it, the Astrometrics room on Voyager looks very much like a bridge, just without a Captain's chair. Voyager supposedly cannot separate. Seven of Nine has engineering, science and navigation-like duties and sometimes does her own thing when the other characters are using the Bridge, so maybe that room is the equivalent to the Battle Bridge on Voyager.
As a side note regarding the article, I don't see how it could have been that the original movie bridge was destroyed. The changes to the rear of the bridge that would seems to be a new set are present in "The measure of a Man," and then changes are made for various ships in various episodes. On the DVD for Star Trek V, Harve Bennett tells reporters in 1989 or 1988 that this is a new bridge for that movie, but it does not seem to be same one from the previous movies, and the bridge from the earlier movies, with its modifications, is apparently seen throughout TNG.
One comments suggests the fore part was
damaged, perhaps, but the smaller (that is to say more ovoid) fore section is seen in "Encounter at Farpoint" and "The Battle," before the supposed damage in the article. This does seem plausible, though.
I could see the movie bridge being altered for the TNG pilot to accommodate a
ready room in the same space, and then not being able to restore its prior appearance.
The Stargazer could have been a Consitution-class, but since it is not, the smaller bridge makes sens with the different configuration of ship. Since the Constellation-class has a larger saucer but not engineering section, a different bridge layout, especially one that can therefore fit more things in the saucer, like a ready-room near the Bridge, works well.
I see the source listed mentioning the destruction of the original set, but based on preponderance of sources like interviews from blu-rays and so on mentioning the continued use of the original bridge set, there must be some confusion here.
EDIT: I wanted to add I still think it is an amazing website