I have more than one version of wine installed and more than one wineprefix. I added a configuration file in each wineprefix that remember the wine version used, and my scripts use that to launch the apps in the prefix with the proper wine version.
Since the wine versions may depend on different wine-mono version, the sharing mechanism would have to allow parallel installation of multiple wine-mono versions, and wine would have to make the prefix link to the right wine-mono shared install. Updating the prefix with another wine version will have to update the wine-mono link to the right wine-mono shared install, when it differs.
Whatever sharing mechanism that will end up in wine would have to handle that situation.
Also, having to use another filesystem type/partition is not a solution. It must work on ANY filesystem used by the user.