I can’t be bothered to fact check your figures but I will assume you are correct.
Transport links to Newcastle and Leeds are not ‘excellent’. Newcastle airport is on the wrong side of Newcastle for it to be truly an airport for all of the north east. Leeds isn’t particularly conveniently located even if you live in Leeds and it is very run down.
But my main point is that you can always construct a case to get rid of regional infrastructure in favour of doing it all more efficiently at a centralised hub.
If all northern flights went from Manchester with all airlines based there I bet the prices would come down sharply. Parking and facilities for passengers could also be brought up to Shippol standard. Yes the Geordies would have to get in the car and drive up to Edinburgh or go down the road to Manchester but so what, they would get soon used to it.