They don't have repeated footage, they're completely sequential. I believe Close Encounters has branching, Gladiator, and Apocalypse Now.

I should note that I believe that the maximum bit-rate needs to be considered when branching is involved. That is, the maximum A/V bitrate for Bluray is 48Mbps. At the point of branching both the current m2ts and the following m2ts files are loaded into memory together for 11 seconds - and even though they're sequential it would appear that the data rate for the final 11 seconds and the first 11 seconds of the following clip should add up to no more than 48Mbps. If the bitrate exceeds 48Mbps when the two parts are added together you would likely experience a non-seamless transition.

This is largely undocumented, and I'm mostly speculating, but I do believe that's how studio discs are authored - the professional authoring software like Sony Blu-print will ensure that the files get encoded to a conforming bitrate. If you want to do it manually you probably need to set the maximum video bit-rate to 20Mbps instead of 40, and ensure the audio adds up to 4Mbps or less. You may be able to join the video together - 20Mbps max 11.65 seconds + 40Mbps max (clip length - 23.3s) + 20Mbps max 11.65 seconds and so on.