I think TfL have misunderstood the situation. There is no difference in charge between taking trains operated by different companies over the same route. The fact that they use different platforms at Clapham Junction is irrelevant.
For this journey (Epsom to Perivale) the avoiding zone 1 route is defined by changing at Shepherds Bush so you don’t need to worry about doing anything other than changing trains at Clapham Junction.
Touching a yellow reader would end your journey and could have serious revenue implications.