Since zircon crystals form during the cooling of magmatic granite, you’re right that you won’t find “native” zircons mixed in with life fossils, if only because life doesn’t colonise molten magma. But that doesn’t mean zircons are only found in or above basement rock. Granitic intrusions into older sedimentary fossil-bearing formations can contain zircons. There are, for example, Cretaceous and later zircon-containing granite dykes and sills intruding into older shale deposits in Myanmar.