I have the same problem. The menu is unreadable in 4:3, the icons are too large. Amibench does not load and freezes immediately after starting. 4:3 is the natural aspect ratio for the Amiga environment, so it would be good if it worked properly.
What do you mean by 4:3 ? That an aspect ration not a resolution, 640x480 is certainly not going to work well but 1600x1200 should be fine, albeit you will have to scroll the menu to see some entries.
AmiBench was demonstrated on a 4:3 monitor at kickstart in Nottingham last year, so there should be no issues with a 1600x1200 mode , you won't get it working on a PAL MODE though ! You may well need to save the screen prefs mode change, rather than USE it to test as a some apps don't yet autoclose with the intuition reset.