No, they are two different ways of accessing the same account. So if you look in the IDE (the web access to your SmartThings account) everything is the same no matter which app you are using.
But the rules engines are quite different and you set up your automations through the mobile app, so different devices are recognized at the app level by the two different apps, which can definitely be frustrating.
There are some people who are using both, especially if they have a Samsung appliance or Samsung smart television, since those don’t work well with the classic app.