It depends on what you will use Reddit Mobile API for.
If you are using it to create an account, you need to be very careful because reddit tracks your every request and can easily tell if you are a human or a robot.
But if you just want to use it for upvotes, comments or simpler actions, you can already do it with reddit's new interface because they use the same GraphQL. There won't be a difference and you won't need to put a lot of effort.