New version of MSP allows Momos to work with MSP and OmniLib.
The thing is, you are detecting if MSP and Py mods are available in update-fixes and creating this new items for science 8 called plate-pack-1.
But, only on update-final-fixes you replace the lead plates ingredient by this new item.
Meanwhile, MSP update-final-fixes already run and due omniLib being present, created the efficiency recipes for science. Since you haven't updated yet the recipe, the efficiency recipes are created using lead plates as ingredients instead of the plate-pack....

Unless there is a reason preventing it, you need to replace the lead plates for plate-packs before the efficiency recipes are created, that is, in update-fixes, after creating the item.