Adding to Johns 'hack' reason for it mattering where the applications are actually stored, the main benefit to the simple drag-and-drop installation method, in addition to being able to move the app where you please, is being able to delete the app in the normal filer way of selecting delete from the menu. The beauty of the system is the application is /just/ another directory in the filer. You don't need another application or system to get rid of something (part of RiscPkg, the uninstaller in Windows etc.), instead even the most inexperienced of users can easily and assuridly get rid of an application.
Anyway, in this sort of situation, rather than arguing the case for keeping things the way people like it, there should be arguments for changing things. 'The issue is quite complex' and 'benefits... from having control over part of the filesystem' hardly seem compelling reasons for change, in my view. It is just /easier/ to write RiscPkg if it does things with symbolic links, or is it actually /better/?