I know you have the mcebuddy metaday dump in beta, but could you also set it up to dump it to plex comskip, and trigger processing.
I did also put feature request in the plex forums, and I know these two apps are competitors, but this would be a pretty awesome feature. That or build comskip in like plex did instead of mark and skip.
I could probably spend a month or two learning how to make my own script to do it, but well, I am paying for plex pass, and now your DVR plus.