J.F.
My little brother used to stand on the seat when he was little. We always knew what he was up to because we heard the pretend sirens at the same time! Lol. There's an uncovered memory!
If he is truly scared of sitting down, can you you slowly train him the toilet is ok? Maybe have him sit on the closed seat, and let him flush it several times? Then maybe have him flush cheerios or something down the toilet? Get him used to the toilet, so when it's time to sit on it, it's not that big of a deal?
Talk to him, and let him explain what scares him? He is old enough where he should be able to do that, right? Maybe he saw/heard about snakes, rats, or gators coming up a toilet?
What about getting some paper seat covers? Would that help him think there isn't a big gaping hole underneath him?
Good luck!!! Phobias are hard to deal with because they are so irrational.