Board Game Arena

It seems the implementation won't let you use a flap/gear space you have already used. For flaps, since they need to be in order, I think this is valid. But for gear, I can't see why it wouldn't be allowed by the rules. It would let you use the Synchronisation special ability in a pinch. Is this on purpose?

Yes, this is by design in the game.

I think thematically, each of the three dice positions represent a different landing gear: nose wheel, left main, right main.