Bonus points are rewarded for every choice you unlock in the flowchart. One full playthrough should get you the 20,000 bonus points you need and achieving trophies will help towards this goal. Replaying chapters and making different choices unlocks points, too.
Once you have 20,000 points, head to the main menu and go to Extras. Then simply purchase things such as artwork, videos, soundtracks, and galleries until you’ve spent the full 20,000. Some extras unlock during the playthrough, so make sure you’re very near the end, or have completed, the game to have enough extras to unlock.