My understanding of the mod right now is it gets "tacked on" to the end of ItemCombos. In fact with 1.1 to make this clear, and make it easier for me to track my own changes, my ItemCombos file only includes the things I've changed. (And it still works.)
Precedence seems to go to the Main.pak already, meaning I cannot actually change any existing recipes - ones that I thought I'd "fixed" I have retro tested and they did not in fact work; fish, dinner not costing the tomato, and so on.
The only thing that might break is if Larian decides to make an official recipe using the same ingredients we've got in the mod, like water bottle + arrow shaft.
At any rate I'll try to keep the mod updated as long as it stays relevant.