Flying units fly over all terrain effects. I would assume they would fly over obstacles that include a troop unit.
Of course you can drop a berry on a rock, if units with climb get destroyed you just forced a god killing game if no one can climb the rock to claim the omphalos.
Why assume when you could read the rules and know? Also why answer when you actually don't know? Is giving an incorrect answer more useful than not answering at all?