And yes, after GNER committed to these 3, and their bid was accepted and the franchise granted, the DfT then allocated the extra paths to others!
No, you're completely wrong here.
The DfT doesn't allocate paths. They're allocated by ORR, which is completely independent of the DfT. The DfT wrote to ORR ahead of the decision, in support of awarding GNER the extra paths.
However, because ORR is a legally independent body and we aren't the kind of banana republic where the government doesn't have to follow the law, once ORR had decided to award some of the paths to GC and HT, that decision was final (or at least, only reversible if GNER could show that ORR's decision was wrong in law).
This was a risk that was well understood at the time GNER signed up for its franchise: ORR has been wholly independent of SRA/DfT throughout the whole post-BR era, and does not make its decisions solely on the basis of the franchising system.
At the time of its bid, GNER could've asked DfT to make higher premium payments contingent on being granted the rights in question. It chose not to do so, and hence deliberately assumed the commercial risk of the ORR decision going against it. Changing the rules once the ORR decision had gone against GNER to reduce the premiums it needed to pay would've been grossly unfair on the other companies who bid against GNER for the franchise.
I doubt it considering they gave us it in the first place, but you may remember certain liebour politions saying they would renationalise pre-1997. Some may say that the major goverment rushed privatisation through to make sure it was complete before the election. Whatever nationalising will cost a lot of money the UK doesn't have.
The Major government unequivocally did rush privatisation through to make sure it was complete before the election - that's not even in question.
And renationalising operational control by not refranchising routes when existing franchises end wouldn't cost the UK anything. The aspects that'd cost money would be 1) terminating franchises that weren't at an end; 2) (much more so) renationalising the ROSCOs.
I'm not sure taking everything in-house would be a good idea: the public sector's hardly famed for its efficiency. But running non-intercity routes on a LOROL/London Buses basis would be sensible (ie the service is controlled by local government, which sets fares and takes revenue risks, and the private company is just a contractor tasked with doing things cheaply to contract).
(it's moot anyway: the Tories aren't ever going to miss an opportunity to throw sackfuls of cash at their mates. We're more likely to see NR carved up and privatised than any kind of sensible policy from that lot)