Your answer to "How will they get to the bottom floor before going through all the others above it" boils down to "Something will happen that makes that true", by that logic why wouldn't they just bring the home center to the top floor through "the same kind of magic BS that already put two girls, one giant store, and a bunch of animals on that floor"? If the story does end up as them teleporting adventurers to the bottom floor, the whole explanation of "The gem that brought the center here is cracked and can't be used again" makes about as much sense as your "answer", so hey maybe you're actually cut out to write isekai

might take some time to work up to that level of conscious thought though