www.makemkv.com

After much research on audio dropout problems on some newer BD disks, the consensus appears to be that it is a problem related to seamless branching. Wouldn't any "branching" be eliminated when makemkv rips a disk and joins the multiple mpls segments into one file? Shouldn't the fact that there is a continuous audio/video file and no longer separate small files eliminate the problem?

Could someone help me in understanding what is going on?

While I can't directly address what MakeMKV does, whenever you assemble a file out of segments that are (potentially) stand-alone, there is some overlap. Some audio CODECs will handle these glitches gracefully, some not so gracefully.