You have ducked my question, which was "[W]here do you think they originated?" as a
people not as a faith.
If we're characterizing indigeneity based on genetic ancestry—which it sounds like you are—then we're going to have to wrap our heads around the
genetics of the Levant.
Not just the Samaritans, though; have a look at
this thread. To the best of my understanding, all of the diaspora Jewish populations tested are related to the fellahin who stayed in the Levant and converted to either Christianity or Islam. As the study authors point out, Palestinians, Bedouins, Druze, and various Jewish populations have a "shared genetic history of related Middle Eastern and non-Semitic Mediterranean ancestors who chose different religious and tribal affiliations." If this is correct, Israelis and Palestinians in the region have essentially the same goal: To construct a new nationalist identity in the region where their polytheistic Canaanite ancestors lived thousands of years ago prior to converting to one monotheism or another and then being subjugated by a series of foreign imperial powers such as the Greeks, Romans, Umayyads, Crusaders, Ayyubids, Turks, and Brits.
tl;dr — If the Jews, Christians, and Muslims of the region are all descended from the same indigenous peoples, then indigeneity isn't going to tell us much of anything about who should live in which parts of the Levant today; we'll have to consider other factors instead.