The bracket for my cb is exactly the same width as the tray but too low, so I made a "spacer" that you can almost see in this pic. Nice thing is, you also can barely see it in real life. The bottom of the bracket is now level with the side of the tray, so you could do the same thing.
Spacer is 4 thick steel washers, soldered together and then painted flat black. Because the tray is black and there is no light, you just see the dark space under the radio if you get down low enough to look back there.
I took the pad out, so that when the radio comes back out, the holes in the tray will be covered.
My antenna is wired under the truck and runs in the grommet by the go pedal, also.
I have since gone to a shorter antenna, but this is much more convenient than a magnetic mount.