Two main reasons: split ticketing and booking fees. Choo Choo automatically checks whether buying two or more tickets covering the same journey works out cheaper than a standard through-fare. You travel on the same train throughout. The app does the checking for you.
Trainline also charges a booking fee on many journeys, typically between 59p and £2.79, depending on the route, ticket type, and when you book. You can see their full fee structure on the Trainline fees page. Choo Choo never charges a booking fee. Trainline was cheaper on 1 route in our test. On routes where prices were identical, both apps are sourcing the same regulated fare with no split ticket saving available.