If you want to keep releasing MP4 files instead of MKV files, that is trivial to do. Because you aren't using soft subs, the only real drawback of MP4 files (their limited subtitle support) isn't applicable here. MKV is well supported, but MP4 is still even more widely supported. So I would encourage you to keep your releases in MP4 to maximize compatibility (or rather, avoid any unnecessary compatibility loss).
Code: Select all
ffmpeg.exe -i input.mkv -map 0 -c copy output.mp4
Xmedia Recode (which is free) also makes this very easy if you just want to use a GUI.
And just out of curiosity, what quality setting/mode did you settle on?