Disable rendering of individual faces (in ArrayMesh)

Help Shaders
1

Godot Version

Godot 4.3

Question

I’m making a tile-based strategy game where every vertex is saved as a height value, so for overlapping areas I would use another layer for part of the terrain. But of course, there needs to be a way to have some layers only cover parts of the world.

The way I had originally handled this is by deleting vertices from the ArrayMesh but erasing terrain this way in the map editor caused huge lag spikes.

So I wondered whether there was some way to disable individual vertices in the vertex of fragment shader.

I tried just using

shader_type spatial;

varying vec3 world_pos;

void vertex() {
	world_pos = VERTEX + NODE_POSITION_WORLD;
}

void fragment() {
	if (world_pos.y < 0.0)
		discard;
}

but (I think because of fragment interpolation) that only gets rid of the parts of the mesh whose y-position is below 0, not entire faces.

So my question is, is there a way to hide individual faces in a mesh without altering the mesh data itself?