Hi,
Non-developer speaking. I think most users would expect clicking an .exe file to result in Wine executing it "as usual", i.e. in the wine prefix pointed to by WINEPREFIX, as if `wine name.exe` were called. Wine should do what the user expects.
Also, not all users want the same things. Different users might want to use different prefix configurations for the same application. The user might want different applications to use the same prefix. Overrides require additional software the user might not want or might not be legally allowed to use.
Compatibility databases already exist in the form of Play on Linux and similar. Their approach seems better. In the long term, users should not ever need them.
Also, application developers should not target Wine. The application should not try to behave differently because it is running on Wine.