On the odd occasion I've claimed compensation for a ticket I've bought using the Virgin app, I use the GWR▸ website for my claim; as far as I know the fact I bought the ticket through Virgin doesn't come into it. Won't that still be the case if I buy through Uber?
For delays you would claim via delay repay of the train company that delayed you. For refunds because of a cancellation and no longer travelling, it goes via the point of purchase.