To put it simply I can remove a recipe using CraftTweaker however I can still craft it using PrimitiveCrafting, following this I'm going to assume that adding recipes will also result in them not being craftable using PrimitiveCrafting.

For example I removed this recipe but it's still craftable using your mod.

there's a config option, so the mod doesn't register recipes on it's own. set it to false, so primitive crafting only uses the recipes you specified in your scripts. Furthermore there's a blacklist and whitelist to remove specific recipes.

I'll look into this further, thanks. While we're on the topic, the configuration option for blacklisting or whitelisting recipes wasn't very clear on what I was supposed to enter, I assume this is just the specific recipes name string?

Yes, this is true. When you remove a vanilla recipe you also need to remove the primitive recipe. This is not a bug. If you want to mass-remove recipes, I suggest making a function that calls both the vanilla recipe removal and the primitive recipe removal.