Update:
Using the Z index feature for some fake 3d gets some spectacular (voxel,vexel?)effects, but it does run into the issue of added objects. To combat this I've changed the plans from filling the entire map with "Nodes" to allowing them to be destroyed. To expedite object culling I've updated the final attack, a bombing run, which instead of just getting rid of a bunch of towers/structures, it now has a great chance of destroying Nodes.
Of course I don't want to punish the player for playing the game, so now I'm thinking of adding another mechanic. One I swore to never do again. Match three.