I don't see why any of that should be surprising at all. It's because nobody cares. All people are interested in is that the trains run. They're not interested in who runs them. They are run by the train people, who are Virgin, possibly, who are British Rail because Richard Branson bought them, or something, or was it Alan Sugar, anyway, it's still the double arrow because that's what's on the sign outside the station. They're no good, anyway, it's late again, and it's bound to be packed like it always is, they ought to sort it out. Greater Anglia? Well they must be part of Virgin, because it's all British Rail, isn't it, so I'll complain to Virgin so it goes straight to the top.
Even for those who do care a bit, it's a confusing tangled mess which keeps changing and you have to care quite a lot to want to bother to follow it accurately.
I've always considered it daft that the TOCs are so obsessed with branding when it's the last thing the actual passengers care about. People want the trains to be on time, comfortable, reasonably priced, etc; they're not interested in what colour they are, and all the branding obsession achieves is to generate comments about "oh, they've changed the paint again" with the unspoken coda that punctuality, comfort, fares and so on have not changed and aren't expected to and why do they keep wasting money on paint. It's particularly irrelevant since for most journeys - especially regular ones - the choice of operator is fixed by where you are and when you need to travel, so you have to catch the 8:32 from Little Wobbley no matter what colour it is this week.
After all, a vacuum cleaner is a hoover, and a ball-point pen is a biro, no matter who actually manufactured the specific items in question.