I shouldn't think the existence of a few lightly loaded services is going to affect the principle of 3tph to Manchester/Birmingham, certainly M-F.
The DfT and Virgin decided to do this on the basis of business need and opportunity.
You can't just divert an odd train to another destination without destroying the service proposition.
Weekend travel is also still a novelty on the WCML after a decade of virtually no-go, and is notoriously peaky depending on sporting events, holidays, weather etc.
Last year's DfT 15-year ITT retained the 2008 VHF pattern, so there is no reason to think they want to change it.
We can all think of lightly loaded trains on other TOCs, even those which are overcrowded at other times.
Very few of the Northern off-peak services I use are busy, but nobody talks about diverting them to other destinations - they are needed to be positioned for the peak.
Some of the emptiest trains in the country operate out of Liverpool St and other commuter terminals at around 0930.
It will be interesting to see if the DfT makes any changes to the various service specs in the extension contracts.