I strongly disagree with this! If the flight isn't interrupted, then it's possible and even necessary to fly over! And the fact that a player somehow obtained the FLY spell (wings) is solely the organizer's oversight and their problem!!!
I will only add that this is not a mandatory rule, but only informational: it says that such restrictions are possible, but the tournament organizer must specify in the rules over which objects it is forbidden to fly. If this is not specified in the rules, then this is the organizer's problem. ;)
I hope for your understanding.
Sincerely.