Quoting Hui on the problem this presents:
"Not in the same folder, the app doesn’t know what resource file to use. MRTCore doesn’t support “..\resources.pri”."
This is a possible customer scenario. Quoting Hui:
"A customer may have an app, then decide to package it."
BTW, it is as of yet unknown if this issue exists only when the to-be-packaged win32 app project is "external".
We suspect it is though because of this: WinUI solutions are also WAP projects and they don't have this issue. In that case though, the .vcxproj/.csproj project isn't external.