In short Manchester isn't a hub for BA, so they apply discounts to route combinations to make it more attractive for people to fly through their hub, rather than take a direct flight.
For AC it's a little less clear, but it's likely that they take the view that routing people through fewer "trunk" routes makes more business sense than through many more thinner routes for their specific fleet make-up and its particular combination of range / passenger capacity & freight payloads and they tailor their fare structure accordingly.
This kind of harks back to the increased use of the 757 on the "long & thin" transatlantic routes from the western edge of Europe to the Eastern coast of the North American continent, as well as the more traditional use of across the width of the USA or Canada. The 757 is a very good fit for these routes and carries a reasonably profitable combination of freight and passengers at an economic hull and fuel cost, whereas a 787 or 737, A321 or A330 would be a bit too big or a bit too small, or not have enough range or even that the pool of passengers & freight between the two points isn't big enough to support regular high capacity service, but is big enough to fall outside acceptability for an occasional or seasonal service.
In short, there are too many unknown factors around routing, aircraft availability, daily passenger loading variations, to make it look like anything else other than an a wholly illogical system.