I do this using dvrmstoolbox but this software is very old. It starts comskip as soon as the recording starts and it runs at a very low level until the recording ends. It works perfect. Comskip has an option for live tv processing. I use Kodi to view recordings and it then reads the edl that comskip created to auto skip the commercial even wile recording.
This is also how I did it when I used Windows Media Center.