Doing some testing. Had to go ahead and buy the combo pack of BD Copy and BD Ripper as my trial period for BD Ripper had expired.
Archived and ISO from the bluray with just the main move and the hd audio sound track. The source disk that has the multi-branching type structure has just a momentary not even pause when it switches from one smaller section to the next.
Took those iso's and made 2 different files. Went to mp4 and selected aac for one, ac3 for the other. Video playback great. 1080p, etc. Audio however a different story. AC3 had serious synch issues about 30 minutes into movie. AAC perfect. It isn't HD audio though. Multichannel but not HD.
Pauses gone during playback.