Is their a way to modulate like on sprites? I want to change the color of the 3d Node individually, so I don't have to make duplicate models to change the skin color. The skin would be gray, but with a tint color applied. Can godot do this? Will I have to create duplicates?

You can do this through a material, by tinting the albedo channel. You can also write a shader, but I think with how Godot's material system works, every object that uses the same material would have the same tint, so I'm not sure there would be much benefit over just using the albedo channel.

Outside of that, I do not think there is a built-in way to tint an entire 3D mesh in a way similar to tinting a 2D sprite using the modulate property. (Though its possible there is and I just do not know or remember)

I find the material has to be made unique. Then change albedo. I don't know what I'll do at this point. I suppose just for body color I can make duplicates.