Thanks, I'm glad you're enjoying it!
It depends on which recipe you're referring to. Creating activated plates from stable plates always crafts at full freshness. For recipes like the science pack, that take in an active plate and spit it back out again, freshness does not pause while crafting; the active plates will keep spoiling while the recipe is crafting. If an active plate spoils during crafting, the recipe will complete normally, and an unstable plate will be returned instead of an active one (the unstable plate will always be 100% fresh).
An easy way to test how the game engine handles these cases is to set up a circuit condition to disable the machine partway through crafting; then wait different amounts of time before reenabling the machine to see what the outcome is.
Let me know if you have any other thoughts or feedback on the planet!