Whole-genome ancestry of an Old Kingdom Egyptian

How do we even know this person was upper class or some itinerant migrant worker that came from somewhere else?

Even the citation claiming the burial method was associated with upper class raises doubts: following the link mentions "pot burial" which has commonly been associated with the poor. The problem with identifying bones with "population" is it often says what the common man was like but not the minority elite that ruled and had power if one isn't careful about who they think they're identifying or the demographic structure of society in these ancient cultures.

Well, I assume the lowest-budget way to deal with a corpse in ancient Egypt is to toss it into the Nile.

More generally, if what you're looking at is a cemetery for the poor, there should be a lot of remains, and there shouldn't be much in the way of decoration. If someone carved a tomb for the remains to be in ("The body was interred in a ceramic pot within a rock-cut tomb"), that already disqualifies them from being poor.