Hey, looking cool. I wouldn’t sweat that much reality. If it looks good, it looks good. Plenty of games have architectural problems that players don’t question deeply. Plus if the time is spent on the ground level then they won’t be seeing the rooftop much.
But if it really bugs you… I’d approach the modular design to this much like a hallway kit. You’ve got a middle section, a corner in, a corner out, and an end cap. Can do no wrong with those four types - essentially boiling the kit down to the smallest pieces possible.