If you have a lot of mods installed, it's not unlikely that both will use the same crafting recipe for something. So what I'm suggesting is simple: add arrows next to the output box in the crafting screen. If you try to use a recipe that is defined in more than one mod, the arrows will appear and you can use them to select what you want. They should only appear if two installed mods have conflicting recipes, however. It could look similar to the trading screen, when multiple offers are available.