Sure you can point everything to everywhere if you have the skill sets and understand all of this perfectly but I believe in keeping everything neat and tidy and all in the same "original" file hierchy. This makes it much easier to later move it again as you do not have to remember where everything is located and what is pointing to what.
I think it is best to put the WP files at the root. And yes, you can change the pointer to where the image files are kept but again all the image files are uploaded somewhere "odd."
I am just saying that the folks who are lost on all of this seem to get it better by having a simple fix for their issue 1.) Prepare your root, 2. Change both pointers in the Dashboard BEFORE moving files 3.) Move all the files, 4. Fix the links.
And somewhere you need to tell folks that when they change their dashboard settings that they lose access to their Dashboard until they move the files. That part is pretty scarey if you are not prepared for it.