Chiltern's website will sell a ticket for Stoke Mandeville to Harrow on the Hill via Aylesbury if you add Aylesbury as a via point.
In terms of the Routeing guide, this is a local journey as Aylesbury is the
common routing point.
The
Routeing Guide in Detail (section F) says at the top of page F7:
Finding a permitted route when the origin and destination stations have a
routeing point in common.
If there is a common routeing point, the permitted route is the shortest route or a
route which is longer by no more than 3 miles. Also permitted is the route followed
by direct trains to and from the common routeing point if the journey is made on
those trains.
(italics mine)
This is a general rule in the Routeing Guide. The "local part" to and the nearest appropriate routeing point of the origin and destination can double back with the mapped route between appropriate routeing points; but the mapped route between ARPs cannot itself contain a double back.
As the Stoke Mandeville ticket permits this double-back, it is actually valid over a longer route than the Aylesbury ticket, not a shorter one. So one could argue the pricing is correct. Usually stations in this situation are put in the same cluster and end up with identical prices though.