At risk of labouring a point there is a fair number of our society (Railpage regulars almost certainly excluded) who do actually want to know the price of a trip from A to B. They will ask at a ticket office or they will ask a bus or tram driver. They are probably expecting a straightforward answer in terms of "$4.50 mate" rather than "It won't cost more than "$4.50 but if you do this and that then it might cost less". Many of us are happy to be able to save a little here and there but we don't ask how much is a cup of coffee and receive a reply to the effect that "It won't be more than $4.50 but do this and pay that first and it can be less".
We here generally have enough understanding of the ticketing systems in use to make best advantage of them. That isn't true of the average Joe who may not be a regular public transport user or might be one of our very many tourists.
I'll use the London example again as it seems to fit. New-in-town tourist walks up to the ticket office at Heathrow tube station and asks "How much to Piccadilly?". There is a fixed-price one-way single-use ticket of £5.50 which is the price he will be quoted in response to that question. He can have a cheaper trip overall by purchasing a Travelcard or Oystercard (at a higher initial cost but allowing freedom to make further trips under the broadly the same conditions as Myki; off peak the Oyster fare is £3.00 for example) but the question is answered fully and truthfully with a specific statement. We cannot do that in Melbourne nor anywhere that Myki now operates.
Actually, there is a parallel with coffee: It won't be more than $4.50 but if you show this reusable card every time, the 10th one will be free!
And I don't understand why you think it's different to London in this example. If you ask how much to Bendigo, you'll be told the headline rate, clearly visible on the fare calculator, as $27. You can have a pass loaded for all or part of the journey, which will reduce the cost, or you can travel off-peak. Other advantages over London (and vline paper tickets) are the ability to go there and back on the same ticket (min 4 hrs for Z1-13), and the unlimited travel after the first 2 journeys (the 2 hr into daily rule). Admittedly not a huge benefit for most people, but the savings would outweigh the $6 myki cost in just one day, and such trips/savings may be useful for shorter segments along the line.
Being able to arrive at the station and hop on a VLine train is a massive benefit for many people. Always being charged the best fare will save people money in many situations, such as buying a peak return paper ticket but taking a different (off-peak) train home because they made other plans during the day, or buying an off peak paper ticket and having to line up again to upgrade to a peak (and then possibly missing that train, and getting the next one, which is off-peak anyway!!).
If your travel arrangements change during the day, then avoiding a peak fare you didn't need to pay would more than cover the $6 myki cost, in just one day (for Bendigo return).
If your point is just that in the London example, there's no requirement to buy a separate card, then I concede only if they plan to totally remove VLine paper tickets. Is this the plan? If so it's still a separate issue to the problem of determining your particular fare, and I totally agree there should always be a short term paper ticket option, or at the very least, make them refundable like everywhere else.