Unfortunately, you're correct: you may have indeed learned a valuable lesson.
The process of restoring a backup to a PS4 is actually quite intuitive, but it follows strict direction in terms of what it backs up and restores. You had chosen to back up only the
PS4 operating system, instead of choosing to backup
Application Data. The data is all the game files needed to run the games.
You had also not chosen to back up your save games. The difference here is that the
Application Data is what runs the games, and the
Save Games are exactly what they say, save games. Saves could potentially be stored in the Sony Cloud for use, but you would likely have had to set a backup there before restoring.
As for the restore process, it essentially does the following; it will wipe the drive, reformat it, and then copy the data back from the backup. This would mean that unless you have backed up the
PS4 System Files,
Application Data, and
Save Games, only your
PS4 System Files would be restored.