It will always be confusing if some fares can be purchased on a train and others can't. If there was a simple universal 'you must buy a ticket before you board', then there would be no confusion (and no excuses).
Quite agree but the industry does not help itself over ticketing.
Although I have not travelled since Covid, my local line Weymouth to Waterloo has TVM's at all stations between Weymouth and Bournemouth and some open booking offices. The guard/conductor whatever they are on SWR normally comes through before Bournemouth and asks if anyone needs a ticket and sells them one without a fuss, penalty fare etc. No idea what happens if you needed him and he was not visible when you get to your destination.
Why do penalty fares only exist in some areas not everywhere?
If that is the only route you normally travel by train then you would rightly think that is the way things are done, so you would expect the same to happen elsewhere in the country.
Rules should have the lowest common denominator and maybe that is not ticket no travel. I would not park a car in a car park with a broken ticket machine so why if the TVM is broken or has a queue why should people be allowed to circumvent it.
Of course confusing rules allows for the issue of penalty fares and fines, so someone benefits from that money. Especially if a TOC is allowed to invent things like a promise to pay that is only valid for one operator at multi operator served stations..