Add more DVR resolution choices to DVR settings. I use HDhomerun and Plex to records news type shows. I don’t need an hour show @ 3-4GB+ on my hard-drive. Furthermore, I really only need 12-14MB per minute of show. 4GB for an hour show is too much for my Windows computer and storage to handle, as Plex is on a second hand computer.
The HDHomerun digital tuners only transfer the digital (HDTV) signal to your hard disk as aired - neither Plex or SiliconDust modify what your antenna or cable delivers.
There is an "experimental* option in PMS to transcode what has already been recorded. This will cut down on the size of each episode, but might take to long or use too much CPU power for it to be with it.
Other than that, it’s not really just your source video is large and other than covering it at recording using the above method (or using a 3rd party app like MCEBuddy) to remove commercials and transcode using your GPU, I don’t think there is anything else to be done.