Plates can be retroactively searched, backtracked, subjects followed back to other cars and tracked back to where they left from, or other cars that are repeatedly in the area prior to cars being stolen before being used for other crimes can be identified and tracked backward. A plate doesn’t need to be flagged prior to a crime. It’s the same way they can tell which tolls and which plate readers a vehicle has passed recently when running a plate, and is frequently used to identify or trip up drug runners.
Translation: you are wrong and seem to be making things up to fit your position, because this is exactly what people have a problem with — that this data is retained regardless of suspicion.