If a non flyer uses reach to melee attack a flyer, the flyer would not be able to counterstrike it's attacker because they are out of range. It would be able to use damage barrier though because that doesn't care about range. I can't speak for arcane wonders, but I believe they want to limit ways to avoid counterstrike in general but especially when associated with guards.
Currently this is a niche situation and wouldn't cause much difference either way. However we have to also think towards the future when more creatures could take advantage. Such as the male force master we think can fly.
