I think that isolating data and applications into 
  their own directory on a PC makes total sense.

Only if you're starting from a position where there is only one kind of application to handle one kind of data. But as a counter example to that, the entire philosophical underpinning on unix is that stuff should be plain text so it can be easily handed between different programs.

I can just imagine the day when I try and pipe the output of one command into another and an ascii paperclip pops up in my cli to scold me for trying to use cat's 'data' with uniq, or something. I shall keep a cyanide pill handy in my desk drawer for such an occasion.