At a guess because FGW does not have an arrangement with SWT? Which is an entirely different situation to the OPs where FCC does have an arrangement with Southern... the clue being in your own words. Of course an appeal will win if their is no arrangement between the TOCs. It will fail if there is an arrangement between the TOCs.
I'm pretty sure that GW 'issued' Penalty Fare 'licences' state that FGW may collect PFs for SW.
I could be wrong - or it could have changed - or something.