Guys, this might be related to US-9 being all kinds of screwed up between the Edison Bridges and where it splits off SR-35 in South Amboy. I’ve taken a brief look at it, but it’s going to take a while to fix up that I haven’t had this week. The route finder algorithm consequently sees the Garden State Parkway as both the faster and simpler (less turns) way to go.
Even fixed up, however, the navigation algorithm is unlikely to tell you to use the earlier exit unless you tell it to avoid all tolls. This is because NJDOT describes US-9 in the area as a non-freeway major arterial, which translates in Waze to primary highway. Compare that the Garden State Parkway, which NJDOT describes as a freeway/toll-expressway, or freeway in Waze, the “fastest route” algorithm will tell you to stay on the Garden State Parkway until the latter exit. It’s a bummer, because I’ve done exactly what you described here many times to avoid the Raritan toll, as I’m sure every other locally savvy driver has, but unfortunately, these kinds of “back way” tricks are often beyond the capability of GPS navigation systems.