Thanks for reporting! This is an awesome report, with all the steps and details and screenshots 
I wonder if it has something to do with AI may stall when ecountering small holes in walls
I think there were some cases where they would stop mining on concave shapes. This might be a fallout from the custom mining tool. I tried to repro, but for the steps 4 and 5 sometimes they weren’t able to finish mining the bottom layer either. 
Since you can keep adding to a mining zone even when they’re already working on it, it’s likely the code doesn’t take into account that they should create a step to be able to mine the top layers, which is probably very difficult to fix.
The mining code was already modified several times before 1.0 because it always had bad performance when mining in water, and we also split big mining zones into smaller chunks (like the builder does) for performance.