Is that when we declare them "indigenous"?

Typically for a culture or an ethnos or linguistic group or some other group of humans, you look to where that group of people first emerged as a distinctive "people" with those characteristics. The Bengali people are indigenous to the Bengal region, for example. There may have been humans in that region before the Bengalis emerged, and there may have been a population of people from which the Bengalis emerged in that area that did not themselves become Bengali, but that's where the Bengali people are indigenous to.

It is a fact of life that pretty much everywhere has been conquered and/or changed hands at least once. It's unreasonable to expect people several generations later to accept being relocated because someone asserts prior indigenousness. Native Americans are not getting back Manhattan (or anywhere else). First Peoples aren't getting Canada back. Aboriginal people aren't getting Australia back. Why should either the Jews or the Palestinians expect their situation is any different? What's so special about either group?

Well, the conflict in this area involves another important issue - self-determination and autonomy. That's different from relocation - which all but the most extreme regard as an unreasonable demand. Instead, it's about whether which of the groups in the region will have the power to govern - the Jews, the Palestinians, both, or neither - and over what territories they will have that power. Unlike your examples of very tiny indigenous populations relative to larger countries, independence and separatist movements can and do succeed all the time. Reshaping political boundaries to create areas where one group of people obtains political autonomy from the larger group or area, like (again) Bangladesh separating from India or (most of) Ireland gaining independence from the British.

And I don't accept that religion is not at the minimum a force multiplier.

No one says religion isn't a massively important factor in the region. Just that Jewish claims of being indigenous do not require at all that one accept biblical accounts. There's massive amounts of actual, archaeological and historic evidence - from both the Roman and Babylonian times - that the Jewish people emerged in the region and are native to it.