If you don't want an .mkv just untick "mux to mkv" in the GUI. After BD3D2MK3D has finished the encoding, fire up tsMuxerGUI.exe in the 'tools' folder in order to author a perfect BD from the .264 video, .ac3 audio and .sup subtitle files which you find in the output folder of BD3D2MK3D.
Just give it a try, it's straightforward.
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