I reread the Inbounds and as I do understand, Isaac hadn't been shaping the rock, he calculated it's cubic content by scanning the rock and did a spectral analysis. So if nitrogen turns the color of this cristal to yellow, it should be also detectable by its spectrum.
As I've read, the crystals are forming strings inside the rock, so its looks to me that they are of natural origin. Vulcanic sounds pretty reasonable to me.
m.f.g.
Xanthos