Does factory privacy glass count toward the tint limit?

Yes. Factory privacy glass is darkened during manufacture rather than filmed, and it's marked on the glass with the word TINTED or the codes AS3 or V. If you apply film over it, the finished result of glass and film together must still meet the legal minimum. And if the factory glass is already below the limit on its own, you may not apply any film to that window at all, including a clear one.