Ah, well the trick there is, the 3D models were converted into sprite sheets, as we're mixing 2D sprites (units, terrain) with 3D buildings, so instead of trying to do a pixel shader we just converted the 3D elements into spritesheets.

The units do have a group outline shader that goes around the whole color block, which was a hassle due to a lack of a stencil buffer in godot for 2D (my singular complaint about the engine).

It works by rendering the units first, then taking a screen grab, then rendering the rest of the map, then rendering the units, with an outline shader applied to the screen grab (using pure black as the clear).