My game has three types of tiles with colliders: pits/flat obstacles, half-height obstacles, and full-height obstacles. The bullets shot by the character are supposed to go over the half-height obstacles, unless he shot fired them while crouching. I've implemented this by having three separate tilemaps. One for ground and pits (with collision layer 1), one for everything that protrudes over the ground (CL 1 & 2), and a hidden one which repeats all the full-height tiles (CL 1, 2, & 3).
Basically, layer 1 is for player collision and the other two are for two bullet heights. When it comes to collision detection, it works like a charm. But I don't know how to make the layer-3 bullets be drawn over the low obstacles without breaking the Y-sorting.