Richmond to Wimbledon is an example of a journey which tests the rules of the PAYG system to the limit. There are numerous routes involving different modes with different frequencies and numbers of changes. I think it's possible that via Earls Court might have been originally shown as the default route because if there is a way of making a journey using only TfL services then TfL tends to favour it. However, that route falls down badly on journey time and the frequencies on the two legs aren't that spectacular either. The vast majority of people will travel via Clapham Junction using SWR and I'm sure that they (or SWT before them) would object to losing out on revenue with the erroneous assumption that the District line is used.
If you use my
fare finder, which uses exactly the same fare data as the TfL finder, you'll find I add information on what zones are covered by each route. This can help to identify what the routes are.
The default route covers zones 2-4 and the fares are consistent with the National Rail scale for 3 zones outside zone 1. Thus it's assuming Richmond to Clapham Junction then Wimbledon. As it's the default route it is also used for any journey not described as an alternative route, even if that route should have different fares. Via Earls Court is an example where the fare should be lower while via Kingston on the direct train should be more expensive (4 zones 3-6). However, there's no way to tell that either of those routes have been used so the default fare is charged.
The alternative routes which are defined are: via Putney/East Putney which is a National Rail through fare using only zones 3-4 and thus slightly cheaper than the default; and a couple of options utilising Underground in zone 1 which both incur the surcharge for mixing National Rail and Underground on a journey including zone 1.