You should not use the expression "direction of a tile" because it makes no sense, as a technical term I mean. Low walls have no direction property (except for repeating them, which is a different thing), so I don't understand what you meant with "I want something like low wall, but for the top, left, and right as well." The term "low" in "low wall" does not refer to the down part of the tile (for the Y axis), but it means below (for the Z axis), and the main purpose of "low walls" is to allow to throw things over them (like arrows and other stuff, but I guess you know all of this).
If you want a 16x16 tile that is traversable on the left side and low wall on the right side, then you should split it as two different tiles. Splitting tiles into smaller ones that have different ground type, as you are now doing, is the correct way to do it, so there is no problem to solve. I think that Solarus v1.6 will have options to lock/fix tiles/entities to the map and to group tiles/entities together, which may be useful to move groups of tiles/entities withouth breaking things too much.