Hi Matteo,
I believe there is a pretty straightforward and standard solution for dealing with these kinds of “home” folder choices on Windows. Most apps use an Environment Variable to specify the path. This allows you to set a default (your installer can set it) but users can always override if they have special needs (like your user who needs to use the user profile folder instead of the more standard ApplicationData location).
In an enterprise environment, most IT teams will have deployment scripts they can use where these kinds of overrides can be easily configured through environment variables.