You are misunderstanding the point. It's not small beer because when you do a large capex programme, part of the return that pays for that is a large fall in unit opex. Generally this isn't achievable as a cash saving, but it is achieved by, say, tripling the numbers of people travelling (more correctly, for the maximum number of people who could travel to triple). In this case the capex has been largely overspent, while the unit opex isn't going to be changed much going from one six car DMU to one five car BMU. In fact it might be worse rather than better. Running an extra train per hour is a very inefficient way to add capacity. It doesn't really matter what the total number of vehicles is because the cost is per seat km provided, it matters how they're used. If you just run more trains with the same average capacity as today, you just increase unit cost in line with supply.
Staff costs between 5-car trains and longer trains have a negligible impact on the cost of operating each seat km.
The capex is what it is. What's important is achieving the best net operating position, or the best affordable combination of net operating position and social benefits. The DfT will run have run lots of forecasts and concluded the the cross sectional capacity need in the busiest section (Manchester - Leeds) will be in the region of 30 carriages per hour. I'm not privy to inside information, so I'm purely speculating based on logic.
It then comes down to a choice of, something like (precise numbers are less important)
- 6tph of 5-car trains, vs
- 4tph of 7-car trains.
It's very plausible that the DfT have found that
- a 6tph Manchester - Leeds frequency generates more punters and more benefits than a 4tph one on the biggest flows
- the staffing cost difference between 4tph and 6tph is small beer
Also, while you focus on core cross-sectional resource efficiency, you forget about periphery resource distribution. I think the post TRU TPE hourly resource distribution is thus
- 2x5car Newcastle
- 2x5car Hull
- 1x5car Scarborough
- 1x5car Middlesbrough
A 4x7car railway would provide 1x7car to each of the 4 arms. This would underserve Newcastle and Hull while carting fresh air to Scarborough and Middlesbrough.
If DfT concluded a 6x5car railway is preferable to a 4x7car railway for the above reasons, then it passes the NCT sniff test.