That reads like a bargaining position. I infer that GTR have objected strongly to the condition of some of the units, hence DfT have now challenged them to explain how and why they cannot accept some units ("beyond repair" is obviously a direct quote of something GTR have stated privately but it seems like hyperbole, i.e. the start of a negotiation). My guess is that a solution will be achieved whereby the DfT, the ROSCO or both pay for the repairs needed and not GTR.
And I do sympathise with GTR on that, they've been foisted with units in poor condition and had several of the excellent 387s moved to their other routes before their replacements are even ready. They're only on a management contract, why should it be on them to sort the mess they've been given.
The second snippet about the "Revised Class 379 Plan" also implies that GTR have essentially asked for (a lot) more money to sort them out, and this document is basically asking "ok fine, how much?"
GTR have gained from the whole DFT position though.
If you look on the GN side, getting rid of the 365s saved on crew training, possibly some station staffing, and no doubt efficiencies on maintenance. GTR have also had the benefit of only having to plan two types of rolling stock for the GN outers, not three, which makes planning and managing the service easier.
They’ve of course also benefited south of the river from being allowed to get rid of the 313s and 455s.
So in that sense having to commission 30 damp and mouldy EMUs that are essentially pretty similar to their existing trains isn’t the end of the world, and of course if they need extra money to do it then all they have to do is go to the DFT.
It’s the passengers that suffer from all of this. Firstly in the form of losing the 365s, and in particular the services they ran, some of which still haven’t returned and probably won’t ever. Then now having to bear all the risks from taking on a fleet which has been stored for several years, and in what it is increasingly apparent was less than perfect storage conditions.
At the end of all this, the GN user is left with a small increase in trains, fewer ironing board seats, and a shed load of risk - with a load of difficulties along the way.