The fleet being in their little hidden pocket forced them to make use of waste materials. I imagine ships sent out on missions also have a duty to collect supplies/energy usable for sustaining the population.

I mean, that's pretty much what life on earth does today. It's not like an apple tree conjures its fruit from nothing. Most biomatter was at one point shit or a corpse. By now, probably both many times over. We just use biological protein reshufflers.