That would be true but for one thing - the stopping service has to run anyway and typically has low loadings. Thus the extra passengers are essentially marginal. That's how Chiltern and WMT can offer low fares.
I agree that if the service was running only for the long distance passengers slower=cheaper would be uneconomic, but that's not how it works.
The cost of adding passengers on a great many trains is essentially marginal.
There are comparatively few trains that are so heavily loaded that passengers are left behind.
Indeed, a standing passenger has essentially zero cost to the railway.
Right now we have Avanti deliberately pricing passengers off of ("peak") trains that run half empty, which are then carried on WMT trains instead.
This might maximise Avanti's farebox, but it imposes substantial additional costs.
Given that the true cost of operating the ICWC franchise (scaling access charges to cover NR's actual costs) is well over double its farebox, I am not sure this is going very well.
Given how low farebox recovery has become, I think cost reductions are likely to be more effective than attempting to squeeze more blood out of the stone on the fares side.
Indeed, i think that on a lot of these journeys, it would be cheaper for the railway and preferable for passengers if one carriage of a Pendolino was fitted with unreserved transverse seating and lots of standing room.
In many cases the journey time advantage would be so large that noone would chose otherwise.
EDIT:
A single vehicle of a Class 710 has 52 seats and ~152 standee capacity, apparently.
As an example, the Avanti vs WMT advantage to Crewe is something like half an hour - I think a lot of people would take it even if it meant standing for the half hour to Milton Keynes Central (at which time enough seats in the rest of the train will have been freed up in most cases).