I've just tried transitioning a few users from Managed Client settings to Profile Manager settings for Mobile, aka Portable Home Folders, and I completely concur... the skip lists are completely ignored. The include lists seem to work, so instead of syncing ~, and skipping ~/Music, ~/Movies, and ~/Pictures, if I just set it to sync ~/Documents and ~/Desktop, that worked, but even the most obvious default skip items like ~/.Trash and ~/Library/Caches were just ignored....
This had worked previously, so I'm inclined to think this is a 10.8.2 / OS X Server 2.2 regression bug. I'll be installing 2.2.1 on my test environment this weekend and see if it's any better there.