Yeah, the transformation of the various sections has been a head scratcher for me. The "baseline" is really just the Discovery-A, which pretty uniformly flew with nacelles detached at STL speeds, but attached them whenever they executed a spore drive jump or standard warp. All other ships of the era until the Athena flew with permanently detached nacelles, which stayed in place even when digging their saucer into a planet nose first (as seen with the USS Antares in "Red Directive").
Here, the Athena was seen retracting her saucer cross bridges when she went into warp in "Kids These Days", but in this episode the bridges were in place at warp when we see the shuttle leave its bay. Meanwhile, the nacelles (which have two distinct kinds of structure, the "feathers" and the nacelles themselves), are always detached, but unfurl into a larger configuration for warp and condense themselves back when moving to STL. Methinks that the cross bridges and the warp nacelle configuration are two separately-managed things, or perhaps the bridges are retracted for transition to warp but can be extended afterwards. Or maybe they were in place because of all the partying and the ship just needed the extra volume for student activities..?
Still, all of this is weird considering the Disco refit ditched her own cross bridges entirely, reducing her overall volume (along with the cutouts in the engineering hull) as well as a convenient way for crew to walk between the sections of the saucer.
Mark
