How do they get to that layout in the first place?
You might set these layouts so they aren't listed in the layout drop down in the status area. Instead, add your own controls for navigating from layout to layout. Scripts can then check access permissions before visibly changing layouts. You can either check their Privilege set name instead of layout access before changing layouts or you can freeze the window, go to the layout, check layout access and then return the user to the original layout before displaying the error message that they don't have access.