I think what happens, is that team team is re-declared with the incoming rider being declared as a "temporary / sort term " signing, specfically to cover for injury.
what this means is that the average of the injured rider, is "protected" within the team .
Tom Perry's average is above that of Josh Bates, so it doesn't matter what average Josh achieves, when Tom is fit to return, he comes back in on the same average he was on before his injury.
It would be different if Josh permanently replaced Tom, as Josh would then come in on whatever average he had earned.
This would only possible because Josh would have started on a lower average than Tom. If Josh upped his and thus, the teams average, that wouldn't be any different to any team member upping there average during the season