It is very clear that running down and closing the lines "not selected for development" was the intention from many instances in the report:
It's no use attempting to deny that Beeching's vision for the railway was of a much smaller network than we have.
I have yet to see any evidence that Dr Beeching ever had a 'vision' of the size of the network that he somehow 'wanted'. That would have been totally uncharacteristic backwards reasoning for someone with the analytical mind of an industrial engineer and senior ICI Divisional Manager.
As has been pointed out, Beeching identified three broad categories of line: (a) those with clear good prospects, (b) complete no-hopers - especially for passenger traffic, and (c) those where things were unclear.
The Reshaping Report had done the sums for the broadly one third of the network (that hadn't already see its passenger services withdrawn in British Transport Commission days) that was generating about 1-2% of the business. I.e. category (b).
The Development of Major Trunk Routes document was about defining category (a) in the light of emerging trends like the growth in oil traffic, imported iron ore, new base load power stations like Didcot and so on. Not all of these routes were necessarily that those had been busiest previously because of various industrial, economic and demographic changes.
The new government had been elected in 1964 on a platform of 'no major closures'. This would appear to broadly have settled things (at least for a time) in relation to category (c).
It would have made no sense to propose or recommend any further withdrawals of passenger services (beyond those in the Reshaping Report) in a document published under the new government.