Once again, the national newspapers don't know how the franchising system works. The last time it was The Times with SWR.
In a franchise agreement there are Change mechanisms if certain things occur or do not occur. One is Infrastructure delay. Most " new" franchises have an "IAD" (Infrastructure Assumptions Document) or "IRAD" (Infrastructure and Rolling stock Assumptions Document) appended to it. This lays out when certain key infrastructure (or rolling stock, if it procured by the DfT) is assumed to be delivered.
If it isn't delivered by that date, Change occurs and the franchisee is financially held harmless through the Change mechanisms. This is because NR Infrastructure delivery (and consequential timetable/stock effects) cannot be a risk that a TOC can take on under the present structure.
The timetable bidding delays have been at the behest of the DfT and the Secretary of State has had to write to all affected TOCs saying that his decision to delay timetables is a "Change" event and therefore the franchisee will be held harmless through the Change mechanisms.
How this works is quite simple. The franchise financial models are re-run to take account of the revised inputs. Negotiating these changes is far from simple as the DfT (and the Treasury) go into some detail here, to ensure they are not getting conned and the TOC isn't trying to load the Change with events that were under it's own control, or had no Change protection for.
We don't see key sections of franchise Agreements (the sensitive bits always get redacted) so we don't know if Northern have strike protection from the DfT for any DOO/DCO dispute. If they have, they will be covered, if they haven't, they will be losing mega bucks.
There are some TOCs that are in near perpetual re-negotiation at the moment, such is the divergence from the original Franchise or Direct Award. GWR is a good example of this.
There is no such thing as a fixed price Franchise these days. Change events are very likely to happen in the majority of franchises so "in-franchise" re-negotiations are becoming increasingly common and, of course, these have to be reported as financial results are declared. The newspapers pick up on this and, for a story, assume the worst.