Sorry maybe slots is wrong term more like landing charges. I do appreciate that yes there is a small amount of people traveling to Manchester from Scotland same as probably vice versa from Manchester, Cumbria & Northhumberland that go North especially during school holidays.
The Scottish Government's aim is to reduce the travel via London which dwarfs the connections through Manchester. It's also to promote more direct flights.
Politically I do have some sympathy with BHX & MAN. The U.K. is an Union of 4 countries therefore Scotland & Northern Ireland have every right to legislate for the better of their respective peoples. Maybe at some point an English parliament will be created that will rebalance the regions of England. London is supported by Westminster and the Crown which will always promote that area.