Pi-hole is just a blacklist of domain names. And if any request comes in for a domain on the blacklist, it sends back an IP of 0.0.0.0 instead of the normal DNS IP for that domain name.
Which means that this would be a similar blacklist for content that comes from ad servers. But instead of sending a false IP like Pi-hole, it probably just uses that check to mark what to skip on playback.
Comskip, on the other hand, scans frame-by-frame of the full video content looking for segments based on resolution, audio volume, channel logo placement, and a number of other factors.