It is Virgin who price both the 'via Long Buckby' and 'Any Permitted' fares (which are available for journeys such as Northampton to Manchester). The 'Any Permitted' fare is pointless for these journeys, because even though it is more expensive than the 'via Long Buckby' fare, still isn't valid via Milton Keynes so has identical routeing!
The Any Permitted fares are, and have always been, valid via MKC - I know because I've used them to get from Northampton to Manchester.
If you want evidence - do a search on National Rail for Northampton to Manchester Piccadilly for Monday.
The 10.25 departure is via MKC with an off-peak ticket of £63.50.
The 10.45 departure is with a change at Stafford, is via Long Buckby only and has a price of £52.60.
The via Long Buckby fares are cheaper, but the challenge you've got is you are usually routed via New Street with a longer journey.
What is needed is for LM to be explicit that any LM only ticket from destinations north of Rugby to Northampton (and vice versa)are valid via MKC and not just Long Buckby - which the routeing guide doesn't currently support.