I personally suspect the engineering challenges might pale next to the challenges of political organization.
Quite simply, the continued human expertise and organization necessary to manage and sustain such a system is far, far beyond anything we have today.
We can't even manage to globally reduce CO2, and the recent government responses to coronavirus have led a lot to be desired, to say the least.
Just because you put people up in space habitats doesn't mean they become any less power-hungry, any more cooperative, or any more peaceful.
You say we'll have the engineering in 1,000 years, and I could buy that. But read Aristotle's Politics from 2,400 years ago, which is concerned mainly with political stability and revolution, and he might as well be describing people today.
I'd like to see us manage "spaceship earth" a helluva lot better before I have even the remotest faith we could manage space habitats politically. Heck, we couldn't even manage Biosphere 2, remember?