No they don't.
The National Rail website will offer a choice of ALL ticket prices from all operators on the route and then give you a choice of ANY operator from which to buy the ticket at that price (you can for example buy a Penzance to London return on First Great Western from Scotrail if you wish).
The only thing you'll sometimes find at the operators own site is promotions such as FGW's current 10% off Advance Purchase fares - but you can still access this by using Nationalrail to find the prices and simply selecting your local operator to buy from when prompted, you cannot buy from Nationalrail themselves.
Never bother with thetrainline.com. You wont get a special deal and you WILL be charged a booking fee.