From what I can see the MakeMKV uses MPEG2 for video and AC3 for audio.
You are misinterpreting, based on your observation of one or two .MKVs that were apparently created using STANDARD DVDs as source material . I'm guessing that if you look at the same "Video File Support" in the section that covers files with 720 (or 756) x 480, you'll find another listing for .MKV files of this nature.
With possible exceptions regarding HD audio formats, MakeMKV does not in any way alter either the video or audio content obtained from the original source material. If a BluRay disc contains H.264 video and DTS audio, MakeMKV will create an .MKV file that contains H.264 video and DTS audio. If the BluRay disc contains VC-1 video and .AC3 audio, MakeMKV will create an .MKV file trhat contains, you guessed it, VC-1 video and .AC3 audio.
I have only used MakeMKV on one standard DVD so far (Avatar)..... its not a Blu-ray version.
If I'm understanding what your saying MakeMKV will transparently pass the orginal video/audio codec from its original container into the MKV container. It will not change the video/audio codec.
So given that the Samsung player will not play a MKV with MPEG2 video codec via DLNA what are my options?
I too have this problem. I tried Handbrake as suggested. It works but it recodes the whole movie, which took 15 hours. The computer is tied that entire time and can be used for nothing else, which results in a hostile wife. There has to be a better way.