No doubt that is the current position. But nobody has justified why these extra powers and national-level consent are required to build and operate, or even just enhance a bit, a railway that is of only local interest, and not an equivalent local road.
So this is a bit of an odd one, and gets into the actual legality of running a railway in the first place. The legality or otherwise lies in the Light Railways act of 1896 and the Regulation of the railway s act of 1840, although both are no longer in effect in this country.
The origins sit in Victorian times, and the necessary stupidity of the system of the time. Private companies had to introduce bills to parliament, and get them passed, in order to be able to raise funds and build a railway. Operating the railway was not covered under this act, instead left to private companies until the regulation act in 1840. This introduced the railways inspectorate, and started governing safety ect.
Fast forward a century and a half, and neither of these laws exist any more. It no longer requires an act of parliament to open a railway, instead being a decision reserved to the Secretary of State for Transport, and the respective devolved administrations. But operating and building that railway still falls under normal planning processes
This leaves a strange situation where the SoS can authorise a railway to be built, but cannot authorise any works needed to build that railway. Railway reopenings go through the normal planning process but this takes a long time. A quicker way of doing this was the Transport and Works Act orders, introduced in 1992, ostensibly for HS1 and the channel tunnel, amongst other important infrastructure projects of the time, but subsequently very useful.
In this process, instead of applying for planning permission from local government, and getting tied up in planning permission for every new signal, platform and bridge, stakeholders in a scheme (including but not limited to Network Rail, Local Government, and grassroots campaigners) can make their application directly to the SoS. This is basically asking for planning permission from central government instead of local councils.
Now, some caveats.
The TWA order doesn't in and of itself grant planning permission. Instead, it's a way of making the planning process less messy, and make it harder to raise objections. What it does do is grant powers to, amongst other things: compulsorily purchase land, use land for access or for a work site, amend or revoke other legislation, close or alter roads and footpaths, provide temporary alternative routes, safeguard land ect.
The SoS then signs off of any TWA order, and any work can start. These are useful for big projects (note HS2 still requires its own acts of parliament die to its immense size) but for reopening local lines, it's still easier, quicker and cheaper to get an order.
Now, onto Nationally Significant Infrastructure Projects. The process of applying for a TWA order doesn't mean that project will qualify as such an important project. That's just an extra level of sign off the SoS can do, which makes it more difficult to raise objections at local level.
The Northumberland line reopening qualifies as it involves creation of new infrastructure, significantly altering roads and footpaths, and the much more intensive use of land that was previously used rarely or laid to waste. We'll still see planning documents in due course, but the order basically allows NR and contractors to go ahead and do anything they need to, to facilitate reopening, short of actually building the stations.