The Reading to Waterloo normal route appears to be closed at Richmond, with the train diverted via Wimbledon.  If that's the case, under routing rules I would expect Reading to Clapham Junction or Waterloo to be offered on the direct train, but if you expand the route further so that it means you have to change trains between routing points, the train that runs via Wimbledon as part of the journey is no longer the shortest route so you have to go via the Hounslow loop.

Where are you actually going - Carshalton?   I wondered about changing you into Trameslink and Wimbledon and send you via Sutton, but it looks like that's closed for engineering too ...

 
tl:dr - online timetabling is becoming more strange.

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This is for Sunday 4th January, out and back in a day. GWR is out of action east of Reading until 11am, while via Salisbury will not work out as Basingstoke to Woking is a bus and in any case the first Sunday train Bath to Salisbury is 09:36.

Leaving aside the ticket, the routing advice from National Rail is... fickle.

Using the 07:58 from Bath Spa, with Clapham Junction or London Waterloo as a destination, the system doesn't mention the direct trains but offers changes at Reading, Basingstoke, with a bus between Basingstoke and Woking, then Clapham Junction at 11:57.

Put e.g. Carshalton as a destination out of the same train, the system offers Reading to Clapham Junction direct at 10.57, so, an hour earlier.

With Clapham High Street as the destination, this throws up a 'Direct from Reading to Clapham Junction' option, but rather than Basingstoke, recommends changes along the way at Staines and at Barnes to give the traveller the experience of travelling via Hounslow and an 11:32 arrival at Clapham Junction.

(Plan 'A' is to ignore the National Rail routing confusion, have a ticket to Clapham Junction and use Oyster from there as it will offer flexibility of route)

Mark