Simply change movement type to Air instead of Land when editing the unit and now you can go over water or mountains. Tested it and works and didn't see it posted so maybe it's not common knowledge.

<MovementType>Air</MovementType>

• AFAIK there are no air units
• It breaks ship transporting if they get air movement
• It's a way to make amphibian units, I was tinkering with it to make my lizardmen mod

You can also play with

    <PassableByLandUnits>1</PassableByLandUnits>
    <PassableByWaterUnits>0</PassableByWaterUnits>
    <PassableByAirUnits>1</PassableByAirUnits>

on terrain types so Air units cannot go over mountains, to make amphibian units

Someone knows if the effect could be applied with a spell? It would be cool to have a fly spell