I ended up not buying the ticket as I had a last minute change of plan. Yorkie does say that if you can get NRE to show it as an itinerary which Barnham to Margate does show via St P then it must be valid however I didn't search for Soton via Barnham to Margate, only Barnham to Margate.
OK - so those weren't Route:Via Barnham fares.
When you mentioned NRE offering the HS1 route for the 'normal' fare for Barnham-Margate in post # 27 above do you mean the via London fare ( which wouldn't be surprising ) or the not London fares ( which would) ?