The problem will come when there is disruption.
I have purchased a last minute ticket, at the station, and been forced to reserve a window seat as they're the only ones left. With me I have a large suitcase, bike and a dog. I've paid £193 under your example to go from Sheffield to Glasgow.
Someone else is booked on the same seat in the same carriage but for the train one hour later. They paid only £5 for their ticket as they have no luggage, no bike and no dog, and they booked under the January sale as soon as tickets were released.
At Carlisle, there is a problem with the train I'm on and we all get turfed off. The one an hour later has someone in "my" seat. They paid a fiver for their journey, I paid £200. What happens?
Next problem is luggage. The later train is full of luggage and there is no space left. What happens to my bike and suitcase?
I remember when reservations cost on top of the ticket price. Was there something that prompted everyone to drop charging for them?
I suspect a single retailer trying to add on charges like that would quickly find they lose much of their customer base to the competition.
Suspect it's because refunding the charge when issues meant the reservation became invalid was more costly/hassle/PR destroying than charging a nominal amount for the reservation in the first place.
Remember you are paying far less for your ticket with the Ryanair model than you are paying for the system we have today. If you want a window seat or even a guaranteed seat of your choice, then you have to pay extra. As for food on the train, to eliminate wastage, only the meals bought before hand are taken on the train.
You should also be able to purchase insurance beforehand to pay up, if the train is delayed or cancelled.
As for luggage, when you pay for your ticket and luggage on the internet you are sent luggage labels (same as the cruise industry) that you attach to your bag. Gateline staff can scan the labels with hand held devices to make sure they are genuine. The gates at stations will be updated to also scan your labels. Unless you have genuine labels on your luggage the gates will not open. You will then be directed to a machine to pay for your luggage but its going to cost you a lot more. Staff on board the train will also have updated hand held devices to scan tickets and luggage. If you have paid for your ticket but have not paid for your luggage online, the onboard host can automatically charge your account as they have your details.
So every station on the network must be staffed from first to last train with a full ticket barrier in operation? Including the stations which only have one or a handful of trains a day/week?
Would be better to do it on the train instead, but one Ryanair flight has about 250 passengers to about 5 cabin staff, maybe 5 flights a day. A Thameslink train has potentially 1000 passengers to zero members of staff, every 15 minutes.
Also, what's to stop me simply saying that I have no luggage when asked by the ticket inspector even though I've bought on one of those £40 bags and hidden it behind other people's bags?
Finally, airlines are point to point, so you check everyone once on departure, that's it. No one else gets on or off during the journey. Obviously not the case with trains. Are you somehow going to do a full ticket inspection between each stop on the line?