Your assumption that TfL and SWT are working together is wrong - at least so far as fare setting goes. And there are in fact four different fares available to you - although only the first two involve a reasonable journey; the two more expensive ones will be slower than at least one of the cheaper options.
State owned TfL in agreement with the Mayor sets fares for journeys that involve only the Underground, the Overground, or both. That's your £3.30 peak fare. There's a political incentive to keep fares relatively low, or you get voted out.
The privately owned train companies jointly (as ATOC) set the rail-only fares. These are also valid for journeys on rail + Overground, as historically the Overground was part of the rail. That's a £3.40 peak fare, but only £2.50 off peak. To see these prices, you'll have to search for a journey from Wimbledon to London Waterloo Rail Station. The train companies are limited in the fare rises they can make to certain fares, I believe including these ones.
To add to the confusion, the train only peak fare also applies in the evening; all the other fares only have a peak time in the morning.
The train companies and TfL both want their slice of the pie on the joint fare, which is the £5.00 one. This is for any journey involving both National Rail and Underground. The fare was really designed for those coming into the rail terminals on the train, then switching to the tube to head into the City (say). The rail companies don't want to accept significantly less from them them than someone leaving the system at Waterloo, and TfL don't want to accept significantly less than anyone else using the tube system (they also want to discourage you from using it for a short journey).
Your final option is the £4.80 one. This one's really two separate fares - a £2.40 Zone 2-3 rail fare, and a £2.40 Zone 1 tube fare - Elephant and Castle and Vauxhall are both on the Zone 1/2 boundary. They could charge you the £5.00 fare for this journey, but I guess they're being nice so they charge you the lower option.