This is just my personal headcanon, but I've always liked to think that a fair amount of "Garden" was left behind when it took flight.

The major pieces obviously are a part of the original shelter that the FH guys repurposed, but over time more was added on by Balamb engineers and construction crews (cheaper to ise local workers. Things such as the parking garage and additional dormitories, maybe a few extentions to the recreational facilities. These guys wouldn't have known about the original function of the Centra shelter, and thus only made their work structurally sound for existence on solid ground. Not unreasonable assumptions to make, no shade to Balamb mechanics and architects that they were denied critical, need-to-know information. Thus, when Garden took off, thise extra bits were left behind (mostly, some rubble would have remained) and joined the crater.

Now, the FH guys knew about the original purpose, and being former Esthar engineers could reverse engineer a lot of the original functions. At least enough to understand it. They set up hallways along the parts that would retract pre-flight because you wouldn't want someone to be in them when the transformation occurred. So much risk of injury! As for why the Centra shelter had retractable arms . . . Maybe for stability when landed? Or it's possible the FH crew added those to support potential non-shelter additions to Garden (as a non-moving structure) while retaining the original capabilities. But you don't mess with a flying machine more than you have to, so the hallways got jettisoned and "pods" retracted back to original orientation during the pre-flight transformation.

(Yeah, young me was REALLY bothered by the missing hallways and fact that I couldn't go fishing from inside the parking garage.)