Something to try in handbrake before trying another program. Go to preferences>Advanced and make sure the minimum length of title to scan (seconds) is set to 10. If it is and you're still having problems, I'd try MakeMKV. Before you have MakeMKV scan the disc, go to Preferences>Video and make sure the Minimum Title Length (seconds) is set to about 10... MakeMKV should pick up pretty much all the title, but the problem with this method is you're admittedly going at it blind. The only way to tell which title's which, I've found, is to open the DVD in the DVD player application and jot down the length of the bonus features you want, making sure to write down the minutes and seconds, then comparing those to the titles listed in MakeMKV's generated list of titles.
Also, I'm not sure if this will work, but you can always try fetching the title # of the features you want through DVD player, opening handbrake, and using the Open Source (Title Specific option) and typing the the title number you want it to scan.