Other way around... you can delete everything in ItemCombos, and just start adding stuff. You can have a one-line ItemCombos to add one recipe that you want in a mod. The stuff in Main.pak's ItemCombos still work - you can't "delete" recipes from Main.pak.

At the same time, it doesn't appear that we really can override existing recipes - at least, you can't shift the order of the ingredients and you can't change the transform keyword. You can change the recipe to produce a new result - like fixing the Magic Big Chicken foot.

My test was the fish recipes. Right now you have to drag the oven (mobile kitchen) onto the fish for the recipe to work. I tried reversing that order and the change would not take. I was getting confused until I tried this with a few other recipes and saw the pattern. Then the kicker was another old fix that I'd put in but never tested: changing the Elven Stew recipe's keyword from Transform1 to Destroy2Transform1. It doesn't work. My version of the recipe doesn't take precedence. The tomato sauce remains. :\