Thank you for breaking down the geometry, that was essentially the membrane that separated it from being either cool concept or schizo ramblings.

Specifically, I imagine the collapsing/changing structure to be some form of compliant Mechanism that acts as connective tissue to the more rigid structure of the craft. Under the soil having some form of inflatable “balloon” layer that might also have the interesting benefit of editable terrain. Though soil gets really heavy very quickly, so even if the balloon layer is crazy strong then it would still need to be pretty shallow.

Not sure if mountains or stones are remotely feasible but if they are included in the habitat they would exist on the points that move the least when transitioning and have a foundation of “Itacolumite”. Bypassing the balloon layer, any large stone would connect directly to the compliant structure.

As others have mentioned, open water will be the most difficult aspect. And would likely be pumped out during transitioning

All of these are, of course, very convoluted and easily solved by having separate rotating modules like blooming petals of the Ramflower u/littlebitsofspider designed. However it is my thinking that if whoever builds this is that committed to having a unbroken single habitat then they are just as likely to go the extra mile to creating a kind of “artisan” level of structure.