First I gotta say I'm loving this mod so much. I've been learning a ton about how circuit networks work so I can build a large scale universal crafter.

I am running into the problem though that many overhaul mods like Space Exploration and Krastorio2 have multiple recipes to make the same item. I also added a mod (Barrel Crafting) that lets you insert barrels of fluid instead of piping it, so there are now over a dozen recipes with duplicate outputs and a few triplicates.

The result is that the Crafting Combinator will choose one of the recipes on it's own with no apparent way for me to tell it to use stone plates instead of wood to craft green circuits (for example).

Can you add some way to blacklist certain recipes without removing them entirely? I would be ok with it being in the mod settings instead of being a per combinator setting.

You can already do this using the dedicated signals the mod creates in the "crafting combinator recipes" tab, just send one of those recipe signals instead of the desired product and it will only set to that specific recipe. If a bunch of recipes have the same name and you can't tell the difference between them, you can feed each one into a recipe combinator in ingredient or product mode to find out which one you want