Doesn't this issue stem from EU competition law?
Anything where an individual taxation authority singles out an individual company (e.g. an airport) for preferential treatment falls foul of being defined as illegal state aid.
It is said that this prevents Westminster from varying APD between locations in England, but doesn't require the Scottish parliament to follow the same rates.
I can see how it could be viewed as "unfair" but you know, frankly that's life.
This is surely just one more illustration of why the Scots wanted a Parliament in the first place.