I sympathise greatly with the OP and is further evidence (if we need anymore) why the ticket system needs a complete overhaul.
The situation regarding advance fares from Manchester to Manchester Airport (and indeed onto Wilmslow) is indeed a joke. The old Northern franchise brought in advance fares on this route in late 2015. As Indigo2 points out above, this is still a
flaw in the fare system that is ongoing.
I travelled from Mauldeth Road to Manchester Airport only last week. I know a single ticket cost £4.40, yet I booked exactly the same train with an advance ticket which covered my journey from Piccadilly to the Airport for £2.90.
I don't have a huge problem with this - the problem I do have is even if I booked an
advance ticket from Mauldeth Road to the Airport on the app, it would have still quoted £4.40 - not the £2.90 despite it being a shorter distance from Piccadilly. Those defending the TOC profiteering from passengers' ignorance on here are in the wrong.