I just completed some testing with Time Machine. The second partition I've been using for my testing was on the exceptions list to my backups, so after making sure one test account's home folder was indeed moved over to that, and the other test account simply had the MobileSync subfolder stored on the 2nd partition, I removed it from the exceptions and forced a couple backup runs. I can definitely confirm that the home folder that was wholly moved over will not back up at all. The MobileSync folder for the other account does get backed up.
So if you plan to use Time Machine, then moving the home folder in its entirety is a bad bad bad move. It's best to stick to moving anything that is large in size, not critical to logging into your account, nor necessary for some of its basic operations (plugins, services, preferences, etc). There are some apps that can give a graphical display of where all your drive space is going to and can be used to help narrow down what can be moved with symlinks pointing the way to where they went.