Actually, don't you have to buy a ticket, and then surrender and pay the difference?
Good luck finding Permit to Travel machines nowadays (in the south anyways)!
There did indeed used to be some sort of 'rule' that said 'you should purchase a ticket to allow you to make part of the journey then change it for the correct ticket at the first opportunity'. I can't remember where I read this but am sure it was not the Conditions of Carriage.
In the case of a priv at an unmanned station and buying a discounted ticket which is not available from a machine then I believe a matter of principle that I should not be left out of pocket by buying a more expensive, full priced ticket (even if it is to the next station). After all, a refund for the difference (no matter how small) will take a while to be processed.
In such instances I never had a problem buying on board and, indeed, SWTs station posters include a 'Buying tickets' section which clearly states 'If the ticket office is closed and you cannot buy the ticket you require from the machine then you should purchase it from the guard on board the train.' or similar wording.
There are also still a few stations on SWT that do rely on Permit to Travel operations - Millbrook is one and, although I haven't read the same poster there, I believe it would say 'Please insert coins upto the cost of the ticket into the Permit to Travel machine and exchange it for a ticket on board the train' or similar.