I use both Mac and Windows machines regularly and I absolutely can not stand the notion that Itunes knows where my music should be and I need not concern myself with it. The same is true for iPhoto. This concept makes it nearly impossible to :
backup data files and be sure they are backed up.
Move data files from one machine to another.
Use another application to view or manage files.
Group files by significance (all the files for 1 project together regardless of type)

I have a paper filing cabinet in my office.
Your idea is equivalent to storing files written in pencil in a separate folder from those written in pen and those separate from files typed.
Ludicrous!