So I noticed when I made smelters for stone > bricks they would often take 2 coal and make coke And mess up the whole line. Is that intended? It picks the recipes automatically.

Hi mate.
I did the coal refining expansion while I was working on the compatibility with Krastorio 2, and since the mod itself gives you the opportunity to decide which recipe you put on your recipes I didn't think that vanilla doesn't allow you to do that.
For now on a Vanilla run I suggest using mods like Furnace recipe selection or something like this one.
In the future I'll implement something like this on my own so you don't have to download 100 different optimization mods.
_77

Cool, thanks for you response and have a good day!

Enjoy ur modded time. :D