Also having the exact same problem. Trying to do just a new writeable for OST and it's syncing every **bleep** folder in the root. I am pulling my hair out trying to get this to exclude correctly.
I've tried custom config files, default config files both on the volume and base image. They don't take effect and in most cases break the logons and don't attach properly.
The documentation is absolute crap on the best of days but for app volumes it's probably the worst I have seen.