First off, MineEstates feels rather undeveloped compared to the sprawling mess that is towny.
Second, Meepcraft is a TOWNY server and advertises as such.
Third, converting to a new plugin would probably mess up a ton of towns.
Fourth, towny is far to fickle to allow much messing with y-coordinates.
The idea sounds fun and gives more options to players, but it would be a gigantic mess many times harder to implement than the API update has been. I don't think it's worth it at all.