I had a similar situation to this recently from Leeds with TPE. I don't think the train was short formed, but it was late, so I (and many other people) were unable to board the train I had an Advance ticket and Seat Reservation on. I was also unable to board the next service, almost immediately behind. I boarded the third service but this resulted in more than 30 mins delay to the overall journey. I wrote to TPE, enclosing tickets and explaining that I had been delayed and why, and pointing out that I had stood for the length of my journey because I wasn't on the train I was booked for, and there were no seats available on the train I actually used, both of which should trigger compensation.
They responded with a lengthy account of why I was not entitled to anything, but then said at the end of it that "In view of your particular circumstances, I am happy to go outside of our normal policy on this occasion and have enclosed £X.XX in Rail Travel Vouchers." They sent me 100% of the value of the tickets. I do wonder if they are just trying to make themselves look generous sometimes...