Given that it's so perfectly aligned with direction of the crystal, maybe it formed from the same solutions as the crystal itself, at the same time rather than quartz forming around pre-existing crystals of something else?
I'm not sure that the black is a crystal. They look round to me (in cross section) I can't see any flat faces like you get on tourmaline. The sides look a bit "fuzzy", almost like small gas swirls on the edges.
they are chlorite inclusions you'll find dark green to red and sometimes rare red and green inside quartz crystals used to look for them myself up near Rushworth Victoria.