You shouldn't find a difference in price between websites, although watch out for where you buy them- I think the trainline adds a service charge and some don't, especially if you collect from a machine. Also some train operators offer things like nectar points if you buy direct from them on their website.
It's worth playing around on something like the national rail website and seeing if you can make it cheaper.
What are the advance ticket prices like? If he can be tied to precise trains and you buy them 12 weeks in advance when they release the tickets that can be cheaper.
Is that a return or 2 singles? If he's travelling home off peak it might be cheaper to get a peak single out and an off peak or super off peak home.
Can you play with the times at all? If he can travel slightly earlier or later it might bring the price down.
There are archaic rules from British Rail days where it can be cheaper to split a journey at an intermediate station, so long as your train stops there. Don't know if any apply to this journey.
Is that the only route he could take? Would it work out any cheaper to do part of the journey by tube and start the train journey further down the line?
Thank you so much for your replies. I like the coach then train option although the downside of course is the risk of motorway hold ups. It might be worth doing that on a Friday when he's just coming home and it doesn't matter if he's late. Unfortunately he won't have any leeway re the time on Monday morning so it looks like we'll have to just pay the fare.