The "Freshness resets on craft completion" only applies to the recipe for crafting hydrogen plate (active) from hydrogen plate (stable). And in truth all this does is prevent the active plates from spoiling while still crafting; without this, if you enable/disable the assembling machine with a circuit condition, it's a bit of a disaster.
For crafting the science pack, the hydrogen plate (active) is supposed to last only a limited number of crafts. Because it's not consumed by crafting science, the faster you make the science pack, the less metallic hydrogen it costs. The challenge is to figure out how to get the most out of each one as you can, while balancing this with the other resource costs.