It's all a complete mess. The mysterious part about theatres and concert venues is the immense number of booking agents who appear to have access to tickets, such that you can buy the same ticket from a number of different outlets at different prices. That made some sort of sense in the historic past, when buying a ticket for a theatre you couldn't make a separate visit to involved stamped addressed envelopes and postal orders. But today, for practical purposes all ticket purchases are either over the counter or online (with telephone booking as a special case of online) and are paid for either by cash or by card. Theatre-land ticket booths for same-day performances are perhaps an exception, as they sell physical tickets for immediate payment, but in general terms the availability of tickets from more than one outlet is a legacy of the past.
To pick up your M&S analogy, it's as though M&S sold their stuff not only through their own shops, but allowed anyone else to re-sell it at margin. That was the original reason for booking fees: you could either buy at face value from the venue, or for the convenience of the tickets being in your city, or available by post, or whatever, you paid a fee (rather than the reseller getting a discount). But then the venues wanted a piece of the action, to the point that "face value" is almost meaningless.
There seems to be a similar netherworld for hotel bookings, but I think the days when some volume travel agents bought rooms at a discount (thus smoothing the hotel's cashflow) and then resold them for what they could get are long gone. I'm never entirely sure quite where Expedia stand in the value chain, for example: is it possible for a hotel to end up with no rooms available over the counter, but Expedia holding an allocation? Are Expedia acting as a principal? Likewise with ticket agencies: have they bought Row C in advance, or are they just dabbling in the same online booking system that the venue's own website uses?
I suspect that in ten years' time, it'll all shake out. Most hotels now have a promise, albeit one for which Hamlet Act 1, scene 4, 7–16 applies, that their online price is guaranteed the lowest with the same book conditions. Airlines are increasingly going direct, and the advantages you get from buying a hotel and airline bundle are rather limited. ABTA bonding isn't worthless, but it's a rather circular benefit as it's usually the bankruptcy of the agent that causes a problem. So probably in a decade's time, theatre tickets will be sold direct, at face value, again.