I plan to implement for TileMapLayer and keep backwards compatibility for TileMap if possible (have to experiment more with #region for whether that can be in the same plug-in version)
There's not direct object stacking in isometric ATM. I can add it to my requested features list though. You're looking for multiple objects to occupy the same square while visually being stacked on top of each other right? (Disgaea turn based tactics comes to mind where you could pick up allies or enemies) If you have an example link, that would help - thanks.