I've run into similar problems, though for one reason or another I don't think I've actually put the zones within the modules, as we are usually doing varying internal layouts as modules in a larger file that contains the parti walls and such. So the zones are in the main file.
That being said the doors in the modules did have to be uniquely identified, so the module ID is used, I have custom labels that recognises a character we put at the end of the module ID, but that's a bit redundant now as 21 has separate data fields for calling them up.
For the zone issue could you use the new 21 text label where you can just select whatever data to display and turn zone stamps off? Although I think I vaguely remember labels aren't allowed to connect to zones.
I made custom zone stamps a while ago too which change depending on the MVO's similar to how TotalZones ones work I believe, you can choose the data you want them to list.
This is one of the most frustrating aspects of archicad, figuring out a way through all the unique limitations of each tool and working around to your desired (or more usually, an acceptable) result.
Best of luck.
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