I consider them indigenous, though you’re correct that they weren’t always there. They were, to the best of my knowledge, the first people to inhabit that place. Much as, where I’m from, Native Americans weren’t always here, but are accepted as the first people.
The Dune wiki, for what it’s worth, describes them as a Native people:
The Dune wiki, for what it’s worth, describes them as a Native people:
https://dune.fandom.com/wiki/Fremen/DE