I dont think anyone was planning on changing the actual partition you want to use. This will still be settable in the config files. But from there on in it will be based on that structure.
I do not think its a good idea to continually change this structure, that is why I believe the most flexible method should be frozen and not altered too much in future releases. I think this code should be backwards compatible somehow with the current setup, as PHP websites often have paths set etc and changing structures around would totally mess with this.