The screen overlay is originally a problem of Android 6. And it happens, if an app requests a permission. The tuner e.g. needs the audio permission.
The reason for this message:
This message appears when you’re running a floating app, and then start a newly installed one, which requests access rights. Floating apps include the chat heads of Facebook Messenger that can appear floating above other. One solution is to grand the permission before opening the tuner. Please go to ‘Info -> Permissions -> Permissions’ and grand the audio permission to smartChord.