The problem is that with years of experience I know that the quickest route at the time the customer arrives at the station is not necessarily going to be the route that you propose being the only permitted route. I also know that not all websites offer combinations of tickets, so your proposals require all train companies to be required to use one of the accredited split ticket engines, which isn't realistically going to happen.
I also know that most people do not leave their house and then do just ONE outward journey and ONE return journey; people often want to stop off at places along the way.
It would be ludicrous to try to restrict car owners to only taking one particular route. Why should rail users have rights taken from them and/or be forced to pay more than the already extortionate high prices?
I also know that during relatively minor disruption customers want to be able to take any alternative route that will get them to their destination without worrying if "acceptance" is in place.
Exactly; people who make proposals that you are doing are creating problems which were not there. However there is no chance of such proposals actually happening in practice as it would be politically unacceptable.
Instead of ripping up the current system, we just need to ensure all flows have "Any Permitted" routeings, ensure that the quickest routes at any time of day are permitted routes (or at least that there is a fare for them) and other tweaks to the current system to protect customers interests.
Introducing a new, anti-customer system and/or a more expensive system is NOT an acceptable solution.
Passengers find the idea that you can use any sensible route to be a simple concept.
It is
not a simple concept to be told that you are restricted to only some of the routes that journey planners come up with otherwise your tickets are invalid. It's also quite stressful for some people.