My imagination says the authors wanted to get ride of that bridge for those reasons...but knew they had to keep it. So they just run with it.
Yamato seems to be able to rest on the third bridge. My guess is it has something to do with their artificial gravity system. Otherwise it would seem odd for the ship to hover without using any thrusters, or maintain relative position with the floating continent in order to blow it up with the wave motion gun. While being within Jupiter's atmosphere.
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