Our users do experience that the audio engine overload message can tend to pop up from time to time. The good thing is that generally this message is not accompanied by any major audio issues.
If you are not having any major audio issues (besides that message itself popping up), we would suggest disabling the pop up.
To disable the pop up, you can navigate to MainStage 3 > Preferences > Audio
Then deselect the check the box next to “Display audio engine overload message”
If you are having audio issues, check out this video about optimizing your CPU.