from what I understand there are little difference between the two. The major difference is the portable store the configurations in pvd folder instead of the install version store them in user's folder.
However, I have tried using both to access my DB from remote firebird server. On one of the parallels (virtual machine) windows 7, pvd portable does not work while installed version of pvd worked.
So I guess there must be more difference in both version than I am aware of.