All this talk about conversions, and nothing has yet been mentioned about source and destination formats. What're we talking here, h264, Xvid? MKV and MP4 are not video formats, they're just container files, which can contain all sorts of different types of video and audio formats.
As for directly switching from an MKV to an MP4, it's a pretty simple matter of taking the video and audio streams out of the MKV file and sticking them into an MP4, no encoding necessary. Whether that would suffice in this case, I dunno.