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I successfully converted the Blu-ray of The Matrix.

The problem is that there are THREE files that are all the same length! ... Does anyone know why this is?

The first two Titles appear to be 100% identical in every way - including audio files, video files, subtitles, and the size of the files. Both of these files have 38 Chapters.

The third Title is different in two ways. First, this third Title is a slightly larger file, because it has an additional audio file that is an additional Commentary. Second, this third Title is just one long Chapter rather than being 38 Chapters.

Does anyone know if there are other differences or why MakeMKV has separated the files like this?

Thank you.

Look at the title and credits sections of each file. You will probably find that one is in English, one in French, and one in Spanish.

When you refer to the "Title and Credits" sections, do you mean while watching the video? Or do you mean looking at something in the file electronically? ... If you are referring to something electronically, can you please tell me where I find that.

Watching the video. In the case of Matrix, the credits in the last chapter are the most likely place for them to have differences, IF the multiple copies is because of languages. Disney does this on a lot of features; not sure about Warner Brothers.

I looked at all three copies of The Matrix and all three copies of The Matrix have the Credits at the end of the movie in English. None of of the three copies of The Matrix appear in any other Language.

Screenshots from my copy of The Matrix (4 disc Ultimate Matrix Collection)
You want source file 00000.mpls.

In all actuality either one of the first two would work if all you want are the English audio and subtitles.
First one offers, in addition to English, French, Italian, Spanish and Portuguese.
2nd choice is strictly English and Japanese.

I see this quite often where the Japanese audio and subtitles are on a separate title and wondered why but never posed the question.