The exceptions wrt MCT for HO is a tremendous revelation, and I believe very few people are aware of it, including apparently the CRS. Kudos to jsloan for finding it.

I think the CRS continues to assume that the MCT is 1 hour, not 3. When the sked change was made, the CRS would otherwise have triggered a warning to the next agent who views the PNR that there is a misconnect. Since it didn't, it's reasonable to conclude that the revised itinerary was still considered as legal. This error might be global and not limited to UA, since the information, which is available in EF, is shared by all airlines.