If the user is trying to install an app, it also has to add that app target(s) to the WineGUI applications list. But then, there is no way to create an .desktop entry of that .exe in order to open native files through the WINE apps (or so far, I'm not able to find it).

For now, Codewavers Crossover can do it. Also on a note, it is able to detect the entire list of project's .exe on its own.

and Bottles too. Works as WineGUI on this, the user has to add the .exe's manually to the list.