I also miss this behavior when using the new Smart Commercial Detection. With Comskip, I was able to mark the end of the previous program and the start of the next program as "commercials" to skip right to the main content when watching.
Since programs sometimes start a bit late, in addition to having padding, this results in parts of adjacent programs being lumped together with the main content when using Smart Commercial Detection. Even if Comskip by default doesn't mark the previous/next programs as commercials, it still adds the cut points (allowing manual marking), unlike Smart Commercial Detection.
However, if there are no commercials between two programs, I can see how it might not be technically feasible to detect that cut point with the Smart Commercial Detection, since the next/previous program is very likely coming from the same domain as before (and not from an ad domain).