Have a similar issue with a couple 4:3 monitors and my main Panasonic TV, and it only seems to happen with a raspberry PI.
I've tried messing with the EDID parameters etc.. to get an under scan, but it never works right..
Quick solution is to use integer scaling for all games of the affected system, and you'll end up with the whole image visible and some under scan.
The best solution is to use a custom aspect ration, keep the integer scaling on, this will keep the image centered so you don't need to play with those setting to center anything.. make sure you start with the "core provided" then switch to custom and just knock off about 10% from the width and height that appear as default values.. You can also play a bit to get more screen coverage while the image still looks good..
Once you're done save the changes as a "game override", so each time the game loads the parameters loaded..
Only issue with this method is you need to do this for each game..