Yes, I use PLEX Dvr… but it shouldn’t matter what you use… MCE is picking up the recording like yours does and then removing the commercials, and extracting the subtitles into an srt file. Then my post process script (that mce buddy runs) is what sets the specific ‘english’ attributes (property) to the subtitles (and I know the audio could be set too) again, not sure mkvedit can do mp4 files, but I’m sure there’s something else out there that can.
Hope that helps, and let me know if you want my script. It's just basically a couple of lines that set the properties of each thing correctly.