As someone who has been involved in numerous construction bids for various companies one rule we always followed was...If we are submitting a non-compliant bid (as an alternative) we always submitted a compliant bid too.
So in this case, what I don't understand is why Stagecoach/Virgin didn't put a price together to cover the pension requirements, then add (say) 20% and submit that bid along with the alternative bid that didn't include the pension uplift.
In this case they can't add 20%, or any other percentage, because the Pensions Regulator has not made any announcement yet on what the additional figure might be. The bidders were being asked to put in fixed price quotes including something potentially hugely expensive which has not been announced yet.
Given that the Pension Regulator is a government organisation, and the DfT is a government organisation, it strains credulity that they have absolutely no idea what the figure is going to be. For businesses like rail it's a huge future risk.
I think the other bidders worked on the basis that they would expect to renegotiate the figure later, which is also not a good way to go about things (if you do construction bids you'll be used to this expectation on occasion as well).
Few bids are ever "totally compliant". There are always some things in the "mandatory" column that you can't, or don't want to, do. Likewise there are parts where the offer can exceed the request. That's why it takes a while to review them all. However, bids also suffer, even at the highest level of management/government, from "bottom right-ism", where the reviewers scarcely look beyond the lowest tender (or highest premium) figure in the bottom right cell of the spreadsheet, and the conditions you put in come second to that. It's essential to minimise that figure as well.