They'd be happy for you to fly as trains between Scotland and London at the busiest times are very full. There is nowhere near sufficient capacity to cater for all the people who would use the train for this journey, if prices were reasonable.
And therefore a making it too confusing is a valid way out. Just make it so confusing, you can't be arsed and just travel a different way.
Like the people on my LNER train a few weeks ago who had paid for weekend first before, so sat in first class on a Thursday thinking it was a standard thing. £170+ each later. They paid, because they were honest people. I think the guard would probably have been ok with them legging it back into standard. At least you know easyjet are going to stiff you £8 for a coffee.
You have to ask whether you are collected a valid economic rent from the service. Or whether you are just ripping off people who have no choice. It is still ripping off, even if the fare is just expensed by people whoose employers ask no questions. (That's not to say that economic incentives for people to travel on quieter servces are not valid)
I remember once, coming back from Edinburgh about 8 years ago. Walk up fare to Glasgow, a night in premier inn and Transpennine Express to Manchester came out at least £100 per person cheaper than an LNER train from Edinburgh. It is all about what you know, tricks and asking for the right thing.
In a way, in 1997 when I used to wander into the station (Huddersfield) and have a chat in the ticket office, before this time is this much, and after is this much. It was a simpler time. Still loads of money.
Another friend (north east based) would walk to the station and ask how much, walk to the car hire place and ask how much, add the fuel, and decide purely on money. The car hire place usually won.
And, it is kind of screwed now, but TP express between Manchester an Leeds was purely a victim of it's own success. 2tph to Liverpool, 30 mins from Hudds to Manchester. Suddenly way more people turn up and it's rammed. You could run the whole timetable with 8 car trains and the would be full.
Interestingly I remember from school French lessons that way back when (i guess 80s or earlier) SNCF used to let you book a reservation on one train and then an insurance train as well in case you missed it (though the tickets were walk up). I forget the word for it though.
We live in such a connected world, where a change of ticket is technically just a click away. On your phone, at a booking office, or a ticket machine.
How you price a change, is another thing. But there is no technical barrier to cancelling a reservation on 1 train and moving it to another.
From an airline perspective, in 2008, I arrived in New Zealand a day late due to a technical problem on the plane. I wandered to the booking desk and said, 'Hi, can I move my flight home a day later because I arrived a day later', `what's your booking reference`, <5 seconds> `all done, here is a print out`
It's about adopting a 'can do' attitude, rather than a 'punish idiots' attitude.