So, regarding this report and a couple of issues raised in this thread...
The pandemic has hit tax revenue hard. But it also hit the farebox hard. The Scottish railway system is funded from a combination of Scotgov subsidy, and fares.
The Scotgov subsidy is calculated as an operational expenditure, partly the money comes from Scotgov tax revenues, and partly from Barnett consequentials.
Reduced government revenues across the board has meant that there is simply less money being spent, as there is less money (real or imaginary) to spend. Scotgov, as well as the UK government, are looking for wars to reduce daily spending, and inevitably, rail is an expensive thing to subsidise, so it takes a hit.
It hasn't helped that passenger numbers are down, so it's not really beneficial to cart empty trains around, and so cutting the number of trains is a reasonably easy way of reducing expenditure. It also saves on staff numbers, which at the moment have take a massive hit, with up to 60% of rail staff self isolating in the week before Christmas.
In Scotland however, the railway system is financed a bit differently. Enhancements to the railway (junction remodelling and station rebuilds) are financed as a funding settlement (a pre-agreed pot of money every year from Holyrood) and NRScot gets to spend that on what it thinks benefits the railway most. They have a checklist to work through, and they're getting down that list. (Note, this is not the same budget as the renewals budget, which is also a yearly funding settlement)
At the moment, the main priority is still electrification and signalling enhancements. Resignalling of the ECML north of Dundee and the Highland Main Line, both to allow closer headways and more capacity, will come from this budget.
In England, each scheme (electrification of the Wigan lines) is funded, approved and signed off individually as its own project. This means you can chop and change them, and they're more easily targeted at swing seats, but ultimately, each project is funded separately. Spending money on Wigan doesn't mean there's less money to spend on Doncaster, you could in theory do both, or none.
In Scotland, all CapEx will be competing for the same budget as Perth remodelling and wiring to Inverness. This is why there is not really any money to extend the Borders line or reopen a line in Aberdeenshire with a dubious business case. If you approved spending several hundred million on either, there would be pressure to reduce the enhancements budget. We've done the north east lines to death, and while they'd be a decent addition in an infinite money scenario, it's not worth it if that would mean not wiring the network that's already there, or increasing the rail subsidy further.
Levenmouth is an odd one. It probably wouldn't be approved today, but it snuck in before covid drastically reshaped the UK economy, and now it's being built, so it has to be funded. As pointed out earlier, it would be disastrous to open a railway line only to not send any trains down it.
Furthermore, as has been pointed out, this list from Transport Scotland has been in the works for about five years now, long before any funding agreement with the Greens was settled. Any announcements on coalition spending commitments will be expected next year at the earliest.
Basically, it's easier, cheaper and more impactful to improve the network that's already there, and link it better with cycle or bus routes, than to commit to spending X million on a new railway, and not have any improvemts to the existing lines.
