This stood out to me, does this mean that FGW is a profitable TOC whereas the "many" others are loss making?
It always was "profitable".
Under the old franchise the premiums were too great for FGW so they terminated the franchise early (as they were allowed).
Last year the FGW premium was £435.6m, but they had a cap and collar subsidy of £266.3m so the net premium was £169.3m.
But that ignores £333.8m for their portion of the network grant (which DfT pays direct to Network Rail ).
Figures from Modern Railways October p32 (originally from DfT
https://www.gov.uk/government/publications/rail-subsidy-per-passenger-mile ).
So the reported £32.3m premium is a lot less than they were due to pay under the old franchise.
But they also have additional costs as well (different access charges, disruption payments, development costs etc), so you can't easily compare them.
I would guess FGW is paying substantially less than it would have done, and DfT is well out of pocket overall, compared to if the old franchise was still in force.
On the other hand the next 2 years will be ones of maximum disruption for FGW with all the upgrade works on the line, and they have agreed to invest more money over the 23 months.
The only profitable franchises (2012/13) if you take the network grant into account are: FCC £68m; Southern £16m; SWT £43m.