>means the app checks to make sure you're not rooted or running a custom ROM
The purpose is to be able to tell if the user is running a version of the app is from the play store or to be able to tell if the device's integrity isn't compromised meaning that it can not rely on the security guarantees the OS provides. Banking apps are not against people using custom ROMs. They just want to ensure they are running on a secure operating system.
And that effect is against custom ROMs and other kinds of user control.