Quote: "seems to be off on the z-axis by the difference in the expected size and the actual size of the terrain."
Do you mean size or position? The rest of your post suggests you meant the latter.
I've never tried moving an Advanced Terrain object so I can see this might be an issue. If the behaviour is consistent then at least you have a solution available.
On your first issue, that's one of the reasons I stopped using Advanced Terrain and started building my own terrains from scratch with a grid of high poly plains as limbs (using IanM's Matrix1 version of
make object plain - there was talk of him converting his utilities to DGDK but I don't recall the outcome

).