https://bugs.winehq.org/show_bug.cgi?id=41275
--- Comment #5 from Michal Suchanek hramrach@gmail.com --- And as the Debian bug report for the same issue suggests this is a bug in the specification so either the freedesktop specification must be changed to work with the extra files installed by wine or wine must stop installing them automatically and only do so on request - probably something like watch the classes registry and whenever new mime type or handler is registered ask the user if it should be registered in the native desktop as well Yes/No/Always/Never. Probably special-casing the default handlers that come with wine is a good idea as well.
The issue is that the user .local files do not amend but rather override the systemwide files for mime handlers, intentionally. You are supposed to select a default application (either by installing gnome or doing a manual selection in .local). For the latter only one of user or systemwide applications are provided as choices for a particular file type - its override, not amend. Same problem with file extensions which do not even have a default. So this is just overall not thought through but does not matter under usual circumstances. It is only problem with wine automatically creating .local mime files.