You can specify the desktop layout settings a few ways. This will help somewhat but its not the complete solution for the warning message you're seeing.
You can do it by GPO but it is enabled for any desktops/apps open in the horizon client. It also blanks out the option to change the layout.
Scripting Definition Settings for Client GPOs
If users click on an icon, you can set it as a parameter:
Horizon Client Command Use
Using URIs to Configure Horizon Client