Is there a better way of doing this render pass approach?

[rosstheblenderanimator]

This method renders the color and base color separately, giving me a lot of flexibility in compositing. I can add blur, glare, and other effects to each layer individually. The downside is that I can only get it to work using a two-layer toon shader.

[Psi25]

i did a similar setup to yours some time ago. that's basically the optimal setup.

if you want to do it faster, the best you can do is to automate it using a python script. I'm not sure how things are handled with malt since buttons and stuff seems to be unique from node to node and material to material basis.