Okay, so OP is back, and I've decided to fill my moat back in and make a better one later.
The problem is that I have no idea how to fill in a channel. I've looked around, and there doesn't seem to be any construction suited for the purpose.
There is no way to fill it with soil again, and there's no way to completely fill it up again. The closest you could go would be to (very carefully, so as to not get cancellation spam) gradually wall in every tile, and then once there's only one open tile left, floor it, leaving one tile of empty space below that floor (you can't wall the last tile because the builder would have no place to stand)
It's true I've never seen anybody walk across treetops in my moat, but that's because I don't let the dang things grow in my moat.
What I have seen is things that get flung, and land on top of the tree, stay on top of the tree. Until I cut the tree down. Others have reported that when living beings end up on top of a tree they stay there until the tree gets cut down. So it's pretty clear things can stay on top of treetops. What isn't clear is whether they can move from treetop to treetop.
Has anybody done experiments on this? Does anybody want to do some science on the issue?
I think that the pathing would be different. Consider how units sometimes get stuck in midair, I think that's the same sort of thing, except less buggy. I assume that next update will have some sort of passable trees with climbing, though. Anyway, it's not that hard to keep trees out of your moat in the first place.