I was working with the 3-BD "Triple Feature" Matrix set that has a UPC of 883929 344536. Everything works fine through MakeMKV and HB.
I wanted to share a little tip regarding the 2nd movie, The Matrix Reloaded. Again, everything processes fine. But if you have your default "title skip" time set to less than about 180s, the default is about 120s, you will get a trailer for the 3rd movie at the end of the 2nd movie. Not a big deal at all, and somewhat cool. But if you did not want that 3rd movie trailer attached at the end of the 2nd movie, then adjust your "title skip" to be about 3 minutes, which is about 180s.