It looks to me like the normal iron plate pipeline is 4 ingot : 40 molten iron : 4 iron plate; but, the iron gear wheel pipeline is 4 ingot : 40 molten iron : 2 gear wheel, which is a 50% discount. Likewise, iron pipe is a 50% discount. I didn't check the other recipes but there may be the same issue elsewhere.

It is not a discount, it is twice as expensive. And it should be since 2 iron plates = 1 iron gear wheel. For pipes it is 1 to 1 ratio

Oh! I see the problem. I have "expensive" settings on this game, and this mod doesn't support it. Then the problem isn't that the cost is off, but just that there's no "expensive" version of the costs in the mod.

Ok, now it makes sense :)
I will update the mod so that it supprts the expensive mode

Thanks!