The standard PF notices at stations state the rules that it is a Pf the the next station that the train stops then the full single fare from the next stop to their destination if continuing their journey on the same train.
It has to be implemented in this way or in some cases it wouldnt be a penalty, take Truro to Padd, if you PF to the next stop (St Austell) £20 then only sell an off-peak from there (think it's around £50) then total fare is £70, which is around £30 cheaper than just selling them an SOS from Tru to Pad which is over £100!
FGW tell us not to PF for Advance tickets on wrong trains, just to charge an SOS, and it suprises me that EMT issued a PF for an Advance ticket, it is a grey(ish) area in the NRCoC along with TOC specific tickets as to be honest they are restricted by advertised restrictions!