One way for a recipe to accept multiple similar items is using the material tags. For example, the weaver does not ask for silkweed in his recipes, it asks for fiber, which can be silkweed, wool, tumbleweed, or even modded items like seaweed and cattail. So you could add your fish item and the recipe could ask for the material “fish”, accepting both items.
There is another way to actually replace things around, which is a little strange but works. You basically mod the manifest of the other mod to make it change your mod.
In this fish scenario, it would work more or less like this:
Create your recipe that uses your item as usual.
Then you create a second version that you want to run only when the archipelago is installed.
But only add the normal recipe to your crafter.
Then in your “mixintos” you add this:
This mean that after you inserted this code into the archipelago manifest, when the game runs, the archipelago will override your recipe with that second version. If there is no archipelago, your mixinto will fail (no errors) and there will be nothing overriding your recipe, so it will be the default one.