There are a lot of things that modify and interact with melee attacks, which we don't want affecting Trample. Not just dice increases, but also things like Battle Fury. It was a considerably varied list, so it was decided that the best thing to do to prevent all of it was to make it not count as a melee attack.
It seems that this may have thrown the baby out with the bath water though, as now the framework for how to conduct the attack is unclear.
For now, the best answer I have is that counterstrikes should work against it, and you have to lose flying to use Trample, similar to a melee attack. Besides that though, it shouldn't be treated as a melee attack. If anyone finds any other weird interactions where it not working like a melee attack causes problems, please let me know.