I think it has to do with the fact that although the actual itinerary is mixed class, it is still a PE fare basis (they have tons of these mixed W-Y fares to cater for the fact that some flights don't offer PE). As such, the website will return it as being valid for travel on PE even if the more significant segment is in Y. There is, like you said, a slightly more expensive PE fare (T class) that has both segments in PE but the website doesn't return it because it is probably only configured to return whichever is the cheaper combination.
Hopefully that makes sense. You should be able to get the call centre to price it if you tell them you would like both segments in T class.