DV in MKV is really the only hope for that - MP4 standards are outside the control of anyone "poor". The most radical change driven by anyone outside the standards body on that front was driven in partby Apple, with MP4 chapters via a special subtitle track in to "m4v" files. Nero introduced a standardized (but not standard) way to put VOBSUB subtitles from DVDs in as a track.
See https://en.wikipedia.org/wiki/MPEG-4_Pa ... ta_streams for what can be in an MP4.