Bowen, I am pretty sure Musical Notes carry through. If you enter your multiball with only one left and you hit it you will get your aab right away. I am 95% sure. But we will test it on ours tonight and get back to you. Edit: Sorry didn't read all of the way through before posting. Thanks @Vengeance for confirming.
We set ours into tournament mode and with the glass off tested to see if the Notes would carry over and they did, so it looks like they do in both standard and tournament settings. We are running 1.68. Also we looked through all of the settings and didn't see anything that mentioned Notes, so I don't think it is a thing that can be changed in settings.
Also for @alveolus, to light the Musical Notes it is slightly different for each song (enough pop hits in You Shook me, left orbit for Warmachine, etc). I always try and pick off a few shots after I have lit the Notes if I know I am going into multiball so that I know close to how many of the five shots I have left to start my aab. Keeping track is good because you don't want to use your aab too soon (though sometimes if you are flailing away at the balls during ball save sometimes you get closer then you think to aab), but you also want it closer then five so that if you need to use a VIP you can get your multiball back if you drain or have one last minute shot to bring it back.