Adspartan will get back the "Save only Current ADT" in the future ;). (Source: #modcraft IRC Chat)
I tested it now in different Ways, there are no duplicates. Also it could be a possibility to do the "Remove Duplicate Models" routine at saving only 1 ADT (Not tested) for 100% safety.
Even if you spawn a M2 (UniqueID: 740) on ADT 1_2 an lay it over to 1_1 and just save ADT 1_2, close Map, reopen the Map an place a M2 on ADT 1_1 it gets a UniqueID of 741. So I expect no duplicates in the future.