It's apparently not nearly as mysterious as I imagine since quartz is the most common mineral on Earth, found in practically every environment and as a component of almost every rock type, making up 12% of the earth's crust. Most quartz is valued because it has no inclusions, but not rutilated...the more gorgeous lines and inclusions the better!
Different minerals can create the lines (called inclusions) within quartz. My favorite is the rock crystal quartz with golden lines, but it can also occur as rutilated smokey quartz and rultilated milky quartz. And less commonly known is a variety known as "tourmalinated quartz" which has black or dark green tourmaline crystals instead of the golden inclusions. I'd love to see some of that in person!
Because there are two different types of minerals (with different degrees of hardness) it can be difficult to get a good and smooth cut. My grandfather apparently has the skill to create gorgeous cabachons. Below is a Rutilated Quartz Cabachon hand cut and polished by my grandfather and grandmother, photographed with some rutilated quartz rough uncut stone. Maybe someday I'll be good enough to try my hand at cutting it!