If regular Comskip was run, it was not on the "do not run list" as you call it. If WE was part of the smart detection, commercial detection would have happened, Comskip would not have been executed, and your logs would have reflected such. So by your own observation, WE is not subject to the smart detection.
What you are stating is that Comskip ran as expected, and you were happy with the result. So what is the issue?
(Since ad networks, streams, and CDNs seem to be shared across a family of networks, it looks like not only would WeTV not be party to smart detections, but all AMC Networks streams: AMC, BBCA, Sundance, IFC, as well as WeTV.)