If I recall correctly Network Rail also have to pay TOCs compensation when they close a station, in this case to alter the track to add the new platform for a number of days, that very likely doesn't come cheap.
You are correct, which can make things look more expensive (since the TOC has signed a contract to deliver those services, so needs to be compensated if it's unable to do so)
This is one problem with people who make comparisons with BR schemes - it was easy for BR to hide the true cost of projects, e.g. they could just scrap the evening service on a line for a year to give plenty of time for long engineering possessions, they could dump the signalling costs onto another project so that the first one appeared to be good value for money. Whereas nowadays things have to be accounted for properly, you have to compensate the train operating side of things (even if that's just another cost centre in the same business).
I'm not criticising the BR approach - accounting was very different back then - but it means that trying to make comparisons to what things cost back then was is always a bit doomed - people like to criticise the modern railway by pointing out that "...but British Rail managed to rebuild/ electrify/ re-model for just a fiver plus a bag of crisps for the engineer", whereas the truth is more like "this was just the net cost of the materials, and everything else was fudged to hide the other costs in other columns".