https://bugs.winehq.org/show_bug.cgi?id=54282
--- Comment #2 from Rafał Mużyło galtgendo@o2.pl --- 1. IIRC, there's already a bug or two on this topic 2. winecfg is a non-factor here; the symlinks happen during shell32 _SHCreateSymbolicLink; desktop files IIRC are written by winemenubuilder during prefix creation/update
Other than that, I agree with at least some of your points - wine's xdg integration is (IMHO) more often than not a misfeature.