After getting the fifth science pack and progressing almost to the sixth, I've noticed I'm not able to produce enough calcium to keep up with demand. I still have quite a lot of stockpiled calcium so I'm not going to run out anytime soon, but... there doesn't seem to be a way to easily waste rare earth in order to balance things out! So I guess you're meant to balance things via careful use of production modules?
The Altered Components recipe that uses the phantom cube to produce N-dimensional widgets and comprehension cards uses double the amount of metal for the same amount of N-dimensional widgets. It helps use up just a little bit more metal.