I agree, I don’t think they’d wait until the last possible moment when the civilization becomes super powerful or builds the mega weapon. I just mention it along the range of development to highlight the why.
I think they might let weaker civilizations keep going, though, just out of hope they wouldn’t be too mean. Also, zapping other civilizations when you don’t need to exposes yourself and your own aggression.
About the shift to VR /computer substrate worlds that wouldn’t have huge footprints, I agree that not all would do that, and it only takes one to go the big building and footprint route and it’s weird we don’t see it.
My guess then would be that maybe they do build big, but they just conceal well..? You get good enough tech at some point you can choose to be hard to see.