Every accredited UK rail retailer, including train company apps (LNER, GWR etc), Trainline, and Choo Choo, receives a standard commission from the Rail Delivery Group on every ticket sold. For non-season tickets sold online, that rate is 4.5%, set by the RDG and the same across all retailers.
This commission is built into the fare itself. It does not appear as a separate line on your receipt, and it does not change the price you pay. The ticket costs the same whether you buy it through Choo Choo, a train company's own app, or a station ticket machine.