The final mux should be/ is .264 file. Only the working demuxed/reencoded file is .mkv, but after rebuild it is converted to .264.
You can check the files with BDInfo to confirm, as it will tell you what the final output is.
Also, check the HIDDENOPTS text file in the zip package of BD-RB, and you can change the intermediate files type.
(MKV_INTERMEDIATE=n, n = 0/1 - 0=OFF (default) - if set to "1", .MKV files are used instead of .264)
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