Nope, it is designed to screw me over. I used to buy tickets from SOP to CTR and start late / finish early at PBL on them if travelling on Sundays
The direct trains rule is in the NRCoC and is unaffected by anything in the Routeing Guide.
However I do not believe it is valid to take a route that is not in the Routeing Guide, and is not within 3 miles of the shortest, claiming you are on a direct train from origin to destination, and then not actually stay on the train to the destination, irrespective of whether or not there's a negative easement, in my opinion (some people disagree).
For example an Edinburgh to Dalgety Bay is valid on the 1708 loco hauled service as this is a direct train. But I do not believe a passenger would be valid to finish 'short' anywhere on the loop.
The direct trains rule is nothing to do with the RG.
I can see the rule being clarified to say that you cannot board/alight at intermediate stations. But, sadly, I suspect some people within ATOC would rather the rule was got rid of completely. Scotrail don't seem to tell some of their guards that the rule even exists, they obviously wish it didn't. But it does, and if there are any plans to remove it, we need to campaign against that.