Obviously you can't.
London Terminals to Birmingham Stations, route Via High Wycombe: can I go via Milton Keynes instead simply because it's a direct train? Of course not.
I agree - Obviously common sense has to prevail - A direct train between two stations is always a permitted route for an "Any Permitted" route ticket, but a direct train between two stations may not be available if the ticket has restrictions (as the example above).
So to quote the Doncaster - Retford example that is an extention of a Scunthorpe - Lincoln service.
The shortest route is Scunthorpe - Barnetby - Lincoln and has a Super OP Return priced at £20.60 Route "Not Doncaster".
The Route "Any Permitted" ticket costs £24.80 and according to the Routeing Guide would be available on:
Scunthorpe - Barnetby - Lincoln
Scunthorpe - Doncaster - Lincoln (JL)
Scunthorpe - Doncaster - Retford - Lincoln (NE)
Nowhere is via Sheffield mentioned as a fare or in the routeing guide maps. It would become a valid route for the journey with a £24.80 ANY PERMITTED fare, but would still not be a valid route with a £20.60 "Not Doncaster" route.
In the same way just the Doncaster to Retford section would become valid with an "ANY PERMITTED" ticket on the direct train via Sheffield, even though it is not mentioned in the routeing guide but would not be a valid route if one purchased the "Hull Trains Only" ticket from Doncaster to Retford.
Stalybridge - Stockport are both routeing points but neither GM or MR maps show the direct route between the two stations as a valid route. It would however be permitted both as the shortest route and by virtue of a direct train.
In absence of a direct train, the following permutations are available according to the routing guide:
Stalybridge -> Victoria -> Piccadilly -> Stockport (Map GM)
Stalybridge -> Guide Bridge -> Piccadilly -> Stockport (Both maps GM and MR)
Stalybridge -> Guide Bridge -> Piccadilly -> Willmslow -> Stockport (Map MR)
I can only find an "ANY PERMITTED" ticket so all should be open.