If I recall, the issue is that you are recording multiple series. And while they all have the same tittle, their SeriesID is different. If that is indeed the root issue, then the issue isn't really with Channels, but rather Gracenote, as they provide the guide data that drives Channels.
I'm not sure that I buy into the argument that recording every occurrence of multiple series and having the DVR maintain only a single recording of all series in aggregate isn't an edge case.
Unfortunately, because of the way that Channels seems to be engineered, it's simply not possible to set commercial detection in the recording rule, because that particular flag seems to be paired with a series. You can either make a recording of each program that falls into your rule with its Keep setting disabled, then change the Detect Commercials setting for that program to Off. After you've done this to each program that will be captured, you can manually delete the now unneeded episodes and adjust your rule's Keep setting. While this is a bit of effort and time initially, it ought to leave the DVR in a state to satisfy your use.