Based on the facts presented, the I-130 and I-485 were denied because they abandoned the process before it was complete. They left, so never got the notification for the interview. Maybe never did biometrics. It's all "abandonment" of the process.
An overstay would have been forgiven, if they completed the process the first time, but they didn't . That makes, as you say, the length of the overstay a critical missing fact.