The great thing about the RiffTrax App is that it can work with ANY type of movie source: DVD, Blu-ray, and even streaming platforms like Netflix, iTunes, and Amazon Video, which is something none of our previous (Desktop-only) apps could do. We've tested with all of the above, and have had fantastic results.
One thing to remember, though: the app is not continuously syncing - doing so would kill your battery! So if you're trying to sync to a different edition from the one we wrote our Just the Jokes commentary to, you may still find that the jokes aren't making sense. (See Independence Day Director's Cut, the Lord of the Rings trilogy extended editions, etc.)
Luckily, the app has a Resync button! So once the "extra" scene has ended, just tap the button, and the app will begin syncing again. In the future, we may create new edits of the commentary tracks to go along with these other versions of the movie. Let us know if there are any you would like to see!