Ah, thanks again for the detailed bug report! One of the joys of working on a game with lots of interacting systems is that fixing one thing often breaks another. It's a bit of a perpetual bug hunting adventure. That said, the issue with Mistral and digging downwards should be fixed now.
While looking into it, I also noticed some related Power calculation quirks when digging upward using ladders with Mistral and general drill tools. It's a minor issue, so I'll leave that one for another time since fixing it would involve deeper code changes.
And yes, now that Alchemist's Pouch blueprints no longer drop in hard mode, the bug should no longer occur in new saves.