Any lucky with this, by chance? I am seeing the call to Plex Commercial Skipper.exe in my logs which creates an .edl file along with a .txt file in the passed-in output directory.
However, the next thing that I see in the log that makes use of that output directory is a segment-list.txt that is not created by the call to Plex Commercial Skipper.exe:
Aug 09, 2019 07:01:55.023 [10228] DEBUG - Job running: EAE_ROOT='\\?\D:\Plex Media Server\Cache\Transcode\Sessions\EasyAudioEncoder' FFMPEG_EXTERNAL_LIBS='D\:\\Plex\ Media\ Server\\Codecs\\dd95667-2434-windows-x86\\' X_PLEX_TOKEN='xxxxxxxxxxxxxxxxxxxx' C:\Program Files (x86)\Plex\Plex Media Server\Plex Transcoder.exe -y -safe 0 -skip_before_video_key 1 -skip_before_inpoint 1 -offset_inout 1 -i "Z:\Broadcasts\Television Shows\.grab\534e840420c28f5ffb7c66e99f635e6bd824905a\segment-list.txt" -map 0 -c copy -loglevel quiet -loglevel_plex error "Z:\Broadcasts\Television Shows\.grab\534e840420c28f5ffb7c66e99f635e6bd824905a\Zane Grey Theater (1956) - S03E26 - The Sunrise Gun-comskipped.ts"
segment-list.txt is not to be found anywhere, so

However, I did find the following script online:
It seems to make use of the .edl file to create a segments.txt. Not sure if that is the same thing, however.
Obviously, it would be incredibly handy to be able to modify the comskip.ini and then rerun Plex Commercial Skipper.exe to see if it identifies/removes missed commercials.