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They don't know what they are talking about. There is no exception for Southeastern because HS1 is a separate route and thus can be charged differently without any problems.
Southern have recently given an instruction to its inspectors to issue Penalty Fares to passengers using FCC Only tickets on its trains.
If they are willing to do this then I would not bargain on the option of a PF on Southern Onlys coming to the boil.
I for one have queried this strongly as I see it as a breach of the Penalty Fare rules and the NrCOC however it would appear that Southern doesn't care about rules!