Prefer the flat directory structure over the hierarchical project structure
I've always aesthetically preferred the hierarchical structure but given how unhelpful it is for new users, and problems that have popped up even for myself every so often (like when a module moves), it's time to acknowledge that it's better to prefer function to form here.
Also the technical limitation I was worried about when I developed this structure doesn't actually apply (that is, the sysadmins don't permit multiple KDE projects to resolve to the same git repository name for other reasons, so I don't have to worry about there being two modules that map to the same 'flat name').
Fixing this for new users is as simple as changing the default option. But I'd want to find a way to automatically move over source/build directories for existing users first.