My thoughts:
I think the idea is alright and that some of the criticism has been a bit unfair.
A - spherical asteroid makes sense. Whoever's building in there want's an efficient foundation in which to build thier structure. Odd shapes would be less efficient and thus rejected.
B - I think it's alright to have a square inside of an asteroid, and build stuff in there. But don't put any towers or anything, because those don't make sense. Unless you're going to have the towers serve as docking points. Also I might add a bit more exterior, not much but just a means for the asteroid to keep track of the surrounding area so it doesn't get surprised and wasted. (some small watching post or something)
C - why would a square be alright? Because we assume that the asteroid is partly hollow in the first place. So they're not hollowing out the whole asteroid, but simply getting rid of the junk inside (the protrusions of rock and such). They're "cleaning up the inside" so to speak. And they'll need mining equipment to cut into the rock for more buildings anyway, assuming that the structures will be mostly within the rock, so they use that same equipment to get rid of the junk. You don't want a piece of rock sticking out break off and smash into a building, or some idiot ram his ship into the rock on his way to a docking point. And last, you don't need to "cart away the rocks". This is space, no gravity (of consequence) just give them a push out the door and no one has to worry about them again.
