A thought - why not run them on to Alton (also a source of much traffic on the A31 into Guildford) so that the trains are at least in motion and (potentially) carrying passengers, instead of blocking platform space/track capacity. Is their sufficient capacity to do so?
I think the timing comes from wanting to connect at Farnham (not Guildford) to the Alton trains both ways. The single line to Alton can only cope with 2 tph if they cross at Farnham, so the Guildford train has to come in about 10 minutes before that and leave about 10 minutes after. (With only two platforms at Farnham, and no turnback crossover, that train has to go out and wait in the depot.) With the run to Guildford being about 25 minutes, when you do the cycle timing sums you have twenty minutes to waste there.
Of course the underlying assumption - the connection at Farnham - is only that, and might be seen as a modest gain driving an awkward bit of timetabling. Unless you are one of its new users, of course; and time will tell how numerous they are.