I don't see any essential problem in magical creatures flying over bodies of water; so long as they don't get near it it shouldn't affect them. I guess Harry is still affected on the boat in SmF because he's still "floating on" the water (though I'd imagine the effect is less than if he were actually swimming in the lake).
It's not an issue with thresholds in the home or church sense; going through the roof would still deal with the threshold (as would burrowing up from below) -- the threshold encloses the home space (or holy space), it's not 2-D.
I'm with you on the home Thresholds being 3-D, but I failed to make that explicit - my apologies for the confusion.
1) When Harry is on a small boat, I think we can conclude that he is still subject to at least some grounding because he is on something very thin which is on/in the water.
2) When Harry is on a houseboat, I suspect the ambient drain on his energy is minimal or nonexistent.
3) If Harry is on a giant tanker/battleship/etc., I would conclude that there is enough stuff between him and the water that I'd consider the ship to be the equivalent of dry land.
Which leaves the following questions:
With creatures flying over water - the limbo contest: "how low can you go? how low can you go?"
With spells cast above water to create effects which pass over that water: If distance drains the effect, what I see is this:
1) determine the initial Encounter Zone
2) determine the ambient Water Threshold value
3) set up Zone Borders in a radius around the initial encounter Zone
4) whenever a spell effect crosses a Zone Border, the Water Threshold is applied as a magical block against the spell
So let's say a Wizard is on a Yacht on the ocean (for purposes of this exercise, he suffers no Water Threshold penalty if he only casts spells within the Zone of the yacht - also "I'm on a Boat! I'm on a Boat!"). Far off in the distance his companions spy a boatload of enemies powering towards the Yacht. Wizard decides to nuke them from afar before they get a chance to attack with any firearms. GM determines that the enemies are about 6 zones away but closing fast. GM determines the local Water Threshold of this section of ocean to be about 7.
So to hit those enemies 6 zones away, the spellcaster would have to overcome about 245 shifts of Water Threshold to affect them.
Ouch. That seems a little much. Any suggestions?
Edit: I think maybe just assessing a flat +2 difficult to each Water Zone crossing will be enough. That brings the difficulty down to 7 plus six Zone borders at +2, resulting in a dampening effect of 17.