I'm a (formerly working) archeologist. Native American land claims are horrifically complicated and way beyond my knowledge, but I'm not aware of anything that's legally based on the scientific consensus about the earliest inhabitants of a specific area. Instead, the term you'll commonly find used is "aboriginal title", which basically just means "we've been here a long time". It's as deliberately vague as it seems and isn't affected by pre-Clovis at all.

NAGPRA has run into complex issues with ownership being unclear when we've found ancient remains, but that doesn't mean people are rejecting the concept of pre-Clovis. It's a separate set of issues entirely.

I'll mention that many indigenous belief systems do incorporate aspects of "we've always lived here" when that's clearly not what the archaeology says. Most such people accept both sides as belonging to separate things in my experience. It's not all that different from Christians who believe Exodus happened for example. The scientific consensus isn't really relevant to that belief and that's fine.

> Clovis-Americans have certain unique rights based on legal theories that their ancestors were the first human occupants of the land

Please point to these rights and legal theories. Do you just mean NAGPRA?

As far as I know, whatever legal rights any native American people have in the Americas at this point in time are based purely on them being here when Europeans arrived near the start of the 16th century.

Whether they had been the occupants for 400 years or 40,000 years wouldn't make any difference to the treaties that were signed (and generally abrogated).