I have a Pi3 running Raspbian. I recently purchased a 7" Touchscreen with a native resolution of 800x480. I went into /boot/config.txt and set my resolution to 800x480 but had black bars all the way around. So I uncommented DisableOverscan=1 and that fixed the top and bottom, but the sides each have about 1/4" wide black bars still. So I uncommented the Overscan settings as well and began playing with them.
I did check, as mine is a NOOBS install, but I do not have the overscan settings on the bottom of the file. They are only in there once. So we can rule that out. No matter what I set the overscan for left and right to, it never ever changes after a reboot. The bars stay 1/4" wide on each side. I have gone from 100 to -100000 with zero change.
But if I edit the top and bottom overscan settings, those work.