At upper right is a piece of babaghoria agate from the Medieval beadmaking center of Limudra, near Ratanpur. It has enough iron in it so that if heated the dark bands will turn red and form sardonyx . The Romans called this region the Sardonyx Mountain . Yes, sometimes, but there are very rare. At right is a piece of natural brown agate used as a blank to make stone blades.
Nothing suggests that it was artificially colored.
It is, however, a rare example. From around the house I lived in for several years in Pune, India. In addition to changing the color of stones, quartz stones have been altered in ways that decorate their surfaces. The earliest of these decorations involves glazing the surface. It has lost some of its glaze.