>>> I booked via National Rail site
You can't actually book directly with ATOC (which runs the National Rail website). The booking facility on the National Rail website directs you to the website of one of the Train Operating Companies (or, if you so choose, a third party website).
The default option for, say, a train from Norwich to London would normally be the Abellio Greater Anglia site but for a train from Norwich to Penzance you might be offered the Great Western Railway website as your first option. (There doesn't seem to be much logic to it though. For some journeys, entirely within the Abellio Greater Anglia area, I've only been offered the websites of other operators to book on!).
So maybe your booking was actually with another company and it's their own rules (rather than those of AGE) which are then applied to your booking?