If I create my own user profile on the server, and put an APP PATH command in it, shouldn't I then only see those projects referenced in the APP PATH when I log into Developer Studio?

Jen,

I'm not 100% sure on this but if you are using Developer Studio it searches all directories in the server approot directory for files with the extention of gfa. If it finds them and the user has read access then it shows in the list of projects. You can use OS level security to prevent unauthorized updating to the directory.