Simple - just don't handle ANYTHING like KSP did. KSP is garbage at handling literally anything that's not a plane or a rocket. KSP 2 is already getting interstellar travel, mega space stations kilometers across, a complete overhaul of timewarp, etc. I don't see why Star Theory should have the same physics of KSP 1, the same UI as KSP 1, have a physics bubble like KSP 1, etc. But then you have to look at everything that anyone wants in KSP 2 like it's going to have the same trash of a physics engine that Squad is happy with for some reason.
I mean, you say that the engine wouldn't be able to handle large structures, but we're getting massive space colonies that should run decently on most computers. You say that such large structures wouldn't be compatible with a physics bubble, but why would KSP 2 want to use a physics bubble system? You say that the UI complexity would be unbearable, but KSP 2 obviously isn't going to use the same UI as KSP 1.
For Kraken's sake, stop going on about these things like KSP 2 will use the same crappy alphabetti spaghetti code as KSP 1.