Manchester to Calgary is a different market than London to Calgary. (and different again for the Calgary to Manchester/London markets.)
In each market each airline will try to find that magic number that takes their particular operation into account. BA being indirect must price their services a little bit lower than a non-stop, or direct airline. If they priced it higher they likely will not get the business. The price from London to the same destination is actually irrelevant to what they can sell in Manchester.
Of course the business/first markets will differ where BA's indirect operation could be preferred to other airlines direct product - FF miles earned, onboard comfort/service/etc. In this case their prices could be higher than the direct, because they know some of the punters will pay ... (or let their employers do so).
Pricing has got nothing to do with costs, it's got everything to do with what the customer will pay. The perfect price is what the customer will pay, no more, no less.