Well, from the looks of it, your status LEDs are shining through a graphic applied over top of the chassis. If the toggle locations do pose a problem you could always use their current holes for the status LEDs, and move the toggles themselves back an inch or so, out of harm's way. It looks like you have the room for it.
Alternatively, play with the nuts for the stompswitches and toggles, so that the toggles are as low to the surface of the box as you can get them, and the stompers as high off the box surface, when pushed down fully, as you can manage.