Unless there is a shuffle of existing, or new resources, I guess that is what will have to happen. You could ask NR for a refund on their GBP 2.6 Billion (and growing) over-spend and ask that those resources be applied. Or could ask that travellers on franchises in the south stop having to cross subsidise provincial franchises and then see if those funds can be utilized. In practical terms the answer is make do with what you have.
I am not denying that the services are overcrowded, I am just asking where the funding will come from; any additional expenditure on rail is taking it away from Road, Defence, Welfare or Health care.
The thing is that Crossrail 2 would allow more trains to run on part of the national network that is paying a premium to the government (even after the NR grant is taken into account).
The maintenance costs of Crossrail 2 would be the liability of TfL, so there would be a reduction in the NR maintenance costs as the shared elements get split between the two.
The network further out (say south and west of Woking) would see more trains which would mean an increase in track access charges but the maintenance costs wouldn't go up proportionally (track replacement would be more frequent, but signals wouldn't necessarily need more frequent maintenance, at least not proportionally to the increase of services, nor would bridges, embankments stations, etc.).
As such there would no more NR network to maintain (although TfL may need to take on some elements or at least share the costs of done elements), there would be more NR income and even the bits of the network that would be busier wouldn't see a significant increase in maintenance costs.
All in all, it is likely that it would save NR money whilst making the franchise more money at a time when the metro services would becomepart of TfL.
One final thought, rail travel may have the same number of people (individuals) using it but still see a reduction in the number of passengers using it. If 100% of commuters used to work 5 days a week but now 95% do with the other 5% working 4 days a week in the office (be that a reduction in hours, withing from home or compressing hours into less days, be that because of children, approaching retirement or just wanting a better quality of life) that would mean that for every 100 people in a train previously there are now only 99. The more the numbers of people who work flexibly guess up the more the numbers of passengers goes down.
Increase flexibly working to 15% and you see a 3% fall in passengers. Increase it so that people are only in the offer 3 days a week and it's another 1% for every 5% of people who do it. It is why Friday morning trains are often noticeable quieter than the rest of the week.
It could very easily be that 5% of people are in the office 3 days a week (2% reduction) and an average of 20% of people are in the office 4 days a week (4% reduction), giving a 6% reduction in passenger demand. That is then coupled with a small increase in rail travel over the same time and the overall result is a small reduction in the number of people traveling.
The very companies that have large (generally) office based staff are the same that are now offering flexible working to all staff, making it a very main stream thing.