Answered: Is there such a thing as "overqualified"?
Or is it just a term made up to find an easier reason to reject job applicants?
So it looks like the consensus is "overqualified" is a euphemism for
"I'm afraid you'll leave this job because I'm assuming you'll have better chances elsewhere" aka "you won't accept being my slave forever due to lack of opportunities"
"I'm afraid you might actually understand how shitty it is here and want to improve things. can't have that"
"I don't want to figure out how much to pay you when you know your worth"
The supervisor/manager doesn't want someone who knows more working under them. Puts their position into question. It's better for them to hire someone who makes them look vital.