When the industry was broken up in '94, the 'major' stations were put under (then) Railtracck management as it was felt there were benefits in operating the largest stations in a common way. This ranged from retail and advertising, to the potential for future redevelopment. Even when Railtrack had zones and regions, the major stations were still run from HQ. The main principle was that it would be more efficient to manage a small number of large stations together under Railtrack, than to have a number of TOCs with 99% of their stations being relatively small and 1 or 2 big ones. Similarly, rebranding a big station in every franchise change would be quite an expensive and largely wasteful exercise.
There have been some changes since then - more stations transferred to NR, e.g. Fenchurch Street, some stations took on train dispatch (Gatwick 4 years ago, Birmingham more recently) and management was transferred from HQ to the NR routes. Retail activity is still controlled centrally, and things like cleaning and security contracts although locally controlled are let centrally to gain economies of scale. As an example cleaning companies will often give a loss leading rate so that they can have the prestige of cleaning, say, Paddington - as it is a good thing to have on their contract record when bidding for other business.
When stations are proposed for transfer between NR and TOC (in the post McNulty world you can expect some of this, in both directions) the costs and revenues are fully assessed and money changes hands. In simple terms, if, for example, NXEA wanted to take on Liverpool St, then the net revenue that NR would forego (say £15mpa) would simply be added to the track access charges to the TOC, meaning in cash terms it is a neutral deal.
For this reason many (although not all) TOCs don't particularly want the major stations, as it is a lot of hassle, and often requires them to have a new set of management capabilities for no real gain.
One final thing, is that where NR beats its retail revenue targets, this profit is then reinvested in the rail network. Where TOCs beat their retail revenue targets, the shareholders get a slightly larger payout.
Incidentally, whilst the retail numbers for the managed stations are quite impressive, they are nowhere near as impressive as BAA who do a similar thing. Liverpool St might make £15m pa, but Heathrow makes £1bn pa with half the number of people passing through. Very different markets, but it does show what can be achieved if you keep your punters waiting for 2 hours. No jokes about performance in East Anglia please!
