Rebuilding strip from clean source doesn't clear it. The copy in the bootstrap seed modifies its replacement, and the replacement carries on from there. The provenance can still look normal.
The paper over complicates what's needed to maintain persistence between the different stages. It's not like the machine is turned off between them. You can simply keep a process running the whole time.
Yes. This is what one wants, since if you have recently rebased it, you're clearly doing work with it. Meanwhile, branches you don't care to touch sink to the bottom of the list.
I think your concrete treehouse counts too though. Add a shower and suddenly you need plumbing, drainage, the structure has to hold more weight. The overcomplicated part drags the overengineered part along with it. They pretty much collapse into the same thing.