If that's how small baby Garnet is, then it might as well be fetal Ruby and Sapphire.

This would seem to suggest that they're made the same way. It would certainly explain Homeworld's intergalactic conquest and the establishment of the Kindergarten(s). Presumably some gems are naturally occurring because they had to come from somewhere, but eventually they decided to start making gems artificially. My guess is that these are exclusively gems like Amethyst and whatever class Pearl is a member of.

Eventually, they ran out of resources, but their greater plans required even more gems. Thus, they set up the Kindergarten. I don't know. This is just me guessing.