Just for the record, I'm not completely happy with the three public methods this class introduces. Personally I find them a bit unintuitive. It feels like they are a bit to "magic". Maybe it's just the method names. They could be a bit more expressive. $tableName should be the first param in my opinion.

It's perfectly fine as a bunch of helper methods inside WikibaseQueryEngine. They do the job and can easily be refactored later. No problem.