As the restaurant analogy is so favoured around here, if you turned up at a restaurant and asked the waiter for a special meal not on the menu, or a mix of side orders and items not on a listed dish and said "You have all the ingredients in other dishes, make this for me" - if the chef had never been asked for it before and does not know how, they are liable to refuse. Also, if the dish has not been analysed in terms of costs, the restaurateur would be entitled to err on the side of caution when working out what to charge the customer.
When it comes to revenue, my aim is to protect the revenue coming in, as that is what ultimately pays my wages. When in doubt, I am prepared to charge, as if the combination is not correct, I seriously doubt that Joe Bloggs is going to write in with a cheque the next day saying he underpaid, but there is a mechanism in place to allow Joe Bloggs to claim back any overpayment (and probably a bit more as well as an apology for the "misunderstanding"). A briefing will ultimately find it's way to the coal-face to say that a potential problem has been flagged up by customer services and the company approach to it is to allow or not, and on past experience, a "please explain" will probably end up in my pigeon-hole as well. (Still, it does give my manager something to read on a Monday morning

)
In the real world, if there are 400+ people on my train coming out of London on an evening, I'm not going to spend 10 of the 15 to 25 minutes I have between stops ringing Control, who are trying to co-ordinate several dozen trains across a large part of the country, to ask if somebody may be free to look up the fares manual to work out if a certain combination is legal or not for just one passenger. (or to take the tickets and issue a UPFN which is also extremely time-consuming). Also, I'm not going to delay the 400-odd passengers (and the equally crowded trains behind) whilst I wait at Reading to work it out after calling the Revenue staff to the train to get their opinion. My starting point is going to be the A to B fare and the more "usual" combinations, and one of the down sides to passengers of using a "rare" combination is that the user can expect to have to argue the legality of it with the revenue staff.
That may not be right in a perfect world, but it's the reality of it.
The analogy was made earlier that if someone pays for three DVD's and the individual DVD's are £4 cheaper than a boxed set then they still have the DVD's to look at, but they can't then complain that they don't have the box. A lot of the split ticketing issues I come up against on a day to day basis are people who want the cheaper fares that split ticketing bring, but don't want the hassle or restrictions this brings. They want the cheaper DVD's but also want the pretty box to keep it all together with. The less you pay, the more potential hassle or restrictions is a maxim of life, not just when it comes to rail travel.
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Interesting little hypothetical question to throw into the split ticketing subject.
Tickets split at Didcot, train reaches Didcot on time, but then delayed for over 1 hour due to signal failure at Uffington.
To my mind it's only the Didcot onwards portion that compensation would be able to be claimed on, as the journey to Didcot was unaffected.
Any thoughts?