I'm assuming you mean the public distribution list builder for Unity and not for Connection?
Currently you have to run it against the local installs on each server - the public DLs are replicated so this can be done. The stored procs for adding users to the dl, at least the last time I checked, didn't allow for passing in the objectID of a user not in the local suscribers table - I can look at a 7.0 system real quick to see if it's still the case or not but at the time there wasn't an easy work around for this. AD manages the DLs, not Unity, so you have to play by their rules when editing them and pushing the changes via the SQLSyncSvr as PDLBuilder does.