I have seen a few rocks and minerals that seemed to show the crystal shape of what they had been growing up against. A good friend of ours found a huge zircon in the New England area with multiple imprints of tiny crystals all over it.
I would think the chalcedony would have formed around the quartz crystal in a totally different period of growth. I believe the size of the quartz crystal would indicate very slow cooling with room to grow the crystal, whereas the chalcedony represents faster cooling with no space to crystallize?