Because of the recipe being enabled, recipes that use iron mechanical parts use it (2 iron > 1 part) instead of the one shown in ui (1 iron > 2 parts) making them 4x more expensive

When mod is loaded by itself Iron-gear-wheel item in all recipes has been swapped with iron mechanical parts and the recipe itself is hidden, not sure what you mean.

the recipe is hidden but not disabled, and because it's enabled from the start in vanilla you can still craft it but it won't show up in the menu. This leads to a firearm magazine costing 4 iron ingots if crafted directly out of ingots, and only costing 1 ingot if mechanical parts are crafted first (you can see the crafting menu showing Unknown key: "recipe-name.iron-gear-wheel" in case of the former)

the recipe is indeed hidden in scripts>data-final-updates>final-recipe-fixes (and a couple of other places) but I can't see it disabled anywhere

Fix in 1.2.38.