There is talk that the next round of franchises will be tied to a cap and collar arrangement based on the RPI rather than just Revenue targets (so that if the economy shrunk they would get more revenue, if they grew faster than the economy the government would recieve higher franchise payments) we will see if that pans out.
As to elements of bids not being carried out the bid is only the first step, once the government chooses one they then enter intensive negotiations on individual services, prices, performance and cleanliness targets, mandatory or optional service requirements, what subsidy would be available for new, more frequent or longer trains, etc... takes months and can lead to tens or even hundreds of small deals with extra government support or franchisee concessions being struck before the final deal is signed. In a way the government is choosing the spirit or feel of a bid before negotiating over the nitty gritty which could produce a result quite different that that in the original bid document itself.
Its like buying a car, first you choose the one you want, then you negotiate on the price, then you customise the optional extras.