Please check your Gantry5 layout settings (base outline). By default, the system message added in the main container, you can move it to any section you wish to improved the look and feel, or you can add custom css code to avoid this issue.
The popup should not interfere with the layout of the website. Please advice.
Gantry 5 system message is not a pop-up or modal alert.
Could you please let me know the result you wish to apply for system message so I can advise ?