It's quite simple: as far as you, the customer, are concerned - Megatrain tickets are a 'promotional' ticket only available through that link. It's not uncommon to have to use a separate link/booking engine/coupon in order to get a discount, is it?
More technically: East Midlands Trains 'sell' tickets en masse to their parent company, Stagecoach. Stagecoach then sell these directly to the customers, often cheaper than EMT themselves can offer.
Worth noting, Megatrain 'seats' do not include any kind of seat reservation (although obviously the idea is that the services Megatrain is offered on you wouldn't need it).