Whilst it’s strictly true, “1 update per 10k rows” is misleading in my view.
When reading that you could easily be forgiven for thinking you could make 10k API calls, and if each call only returned 1 row then that would be a total of 1 update. But that’s definitely not the case.
A better way to put it is “One update per call, and each call will return a maximum of 10k rows”.
And yes, the Query API has nothing to do with the Query column.
That surprises me. I’d suggest having a close look at how you are using that. As I said, you should be charged one update for every query API call that is made. Assuming that you have logs, it should be easy to cross check this.