Well, as Clarence Yard reminds us (above), this one has been in the works for a long time. c.£1m per vehicle per year seems about right for the combined leasing/maintenance costs for the IEPs: mega, but itv tems from the requirements placed on suppliers in the original procurement. (Unfortunately didn't stretch to nice seats in the case of the GW ones...!) DfT have been determined to put in place something close to the East Coast IEP timetable (3tph to Newcastle, 4 hours to Edinburgh) envisaged in the procurement (note that the trains are effectively on a 'take or pay' basis, ie. no money back for running fewer or for less miles, for the next 15 years or so) to justify the contract. The operational cost (staff, variable access, juice) per extra train-km in the Dec 25 implementation is not cheap so one would perhaps imagine widening losses for some time.
The thing to consider is that, given that track access rates and IEP lease charges are essentially fixed (nothing much that LNER can do about them), the more useful measure could be the amount of revenue they can earn compared with staff, EC4T, catering and other directly variable opex. That's really where the idea that 'LNER is paying its way' is coming from (and is broadly correct if fixed costs are disregarded).
Worth noting that if you look at all of the TOCs combined, based on the ORR data set, the extra revenue that's come in for the past 15 years has been more than matched by extra operating costs by TOCs (new trains, staff levels, pay rates, EC4T, maintenance of their stations, paying NR for use of the major stations). Much of the increase has been about providing a better quality (better trains, much more visible staff, cleaner stations/trains and better info through websites, apps and station displays) but this hasn't been matched by more demand so, given GBR seems is expected to improve quality further (certainly a valid choice to make, surely?) one perhaps might expect the net cost of passenger rail to increase a bit more yet....
One thing going the other way is saving the need to pay Corporation Tax: once LNER (and other operators) get absorbed into GBR, its passenger operation will presumably be substantially loss making overall and therefore will no longer be liable for this....