Interesting write up, a not comparable example as my house build was nothing like this scale or cost (I imagine), but during building our house it was interesting to observe where problems came from and how they could be fixed.

The architects -> engineering -> builder handoff is obviously the most lossy, tons of context/intent/purpose is lost in these steps, and normal way incentives align doesn't help with each group being sympathetic to the greater mission, the more they care or clarify etc the more time things take / cost incurred. It is natural to assume everyone is thinking the same as you and will be motivated because you are paying them, but they rarely are, they care less about the result than you do so staying on top of the details you care about throughout the process is a must.

What worked great for us was to have the builder part of the architecture design process and inject their learnings of how to actually build the thing along the way, rather than trying to bolt it on at the end. This isn't normally the way things work as normally architectural drawings are a primary input to a tender process to find a builder.. so is a bit cart before horse but we already had a builder so could avoid that.