We've previously had this very issue.
Myself (and I think one other person) advanced the viewpoint that because NRCOC clause 13 a (I) is excluded from 13c that 13d also doesn't apply to direct trains.
I won't argue with people here, however I will reproduce the text and let you make up your own mind. I have done Sheffield-Leeds on a direct train that passes through Doncaster using a route not doncaster ticket many times. It is advisable to check with the EMT or XC guard on boarding.
13. The route you are entitled to take
(a) You may travel between the stations shown on the ticket you hold in:
(i) a through train;
(ii) trains which take the shortest route which can be used by scheduled passenger services; or
(iii) trains which take the routes shown in the National Routeing Guide (details as to how you can obtain this information will be available when you buy your ticket).
(b) If you are using a Zonal Ticket you may travel in trains which take any route within the zone or zones shown on the ticket.
(c) Together, the routes referred to in (a) (ii), (a) (iii) and (b) above are the permitted routes.
(d) The use of some tickets may be restricted to trains which take:
(i) routes passing through, or avoiding, particular locations; or
(ii) the most direct route.
These restrictions will be shown on the ticket.
(e) If you make your journey by a route other than those referred to in (a) and (b) above, you will be liable to pay an excess fare. This excess fare will be the difference between the price paid for the ticket you hold and the price of the lowest priced ticket(s) available for immediate travel that would have entitled you to travel by that route.
(f) For the purposes of this Condition, a through train is one which may be used by a passenger to make their entire journey without changing trains.