It's a shame that I still have not started my maker yet.
What you can do for the addon list, is discover all files in the add-on folder (and verify them so they aren't causing trouble) and add them to a list, use the list to create a bunch of checklist controls, and then do all your calculations there
Same for music, discover all oggs in the music folder, check if they can be added, and do the same as above.
Pretty sure that's how I did it on my older maker.
For the other method (save as current add-on prefs), you could read the ADD_ON_LIST.cs and the MUSICLIST.cs (whatever the name is) and add them if they are "1", although it's recommended to use the solution with this above and use getSafeVariableName to see if they match the same file. I'm sure there's a better way to do this part, this is just the quickest way I can think of.