What's the plan for open source GDS patches, for fixing the spots where the automated tooling falls down?

AFAIK you just ship the fixed up GDS that's it.

Well. I foresee a large https://wiki.debian.org/FTBFS cleanup effort in the future :)

Even with FGPAs rebuilding an identical bitstream is sometimes a challenge with the randomness involved ... here it's an order of magnitude worse.

Okay. Maybe the far future. 😝