Question
My resource pack that I made for Optifine (ZLTweaks) has grass overlays to other blocks. This isn't special, but I also have a second overlay for the block the grass is spreading to in order to add a sort of shaded edge around the grass, making it look like there's some depth.

These are some old examples, but they show it off well enough for this question.

The only reason a second overlay was required is because I needed the initial grass texture to maintain its biome-coloring, and then the shadowing needed to just be a standard, unshaded texture. Can I achieve a similar effect with fusion? It's the only reason in any/all iterations of non-Optifine CTM that I haven't switched over.

There's nothing preventing you from having multiple connected textures in a model, thus you can indeed have multiple overlays.
In vanilla, tinting of textures is hardcoded per block and Fusion currently does not have a way to change the tinting of a texture.