Isn't it more likely that it's corporate box holders who are the source of these agency tickets? They can apply for up to 10 together at a time and use that income to offset the initial cost of buying the box.
The majority of these top-end boxes are used by companies for entertaining clients, and there's not much corporate entertaining to be done in the away end at Burnley, for example, so they apply for part of their allocation and sell them on.
The club then turns a blind eye because they frankly couldn't give a shit where Burnley's ticket revenue comes from and they don't want to get on the wrong side of their biggest corporate clients. Letting them do this costs City nothing, but pulling them up on it could cost them hundreds of thousands of pounds (if not more).