As an update I installed the Pixel desktop and started Amiberry from there. I created a hardfile and installed WB3.1 on there and installed whdload. When I run AGA games from the Worbench OS, I do not have this issue where the AGA games are bigger than the LCD. So there must be some setting when running whdload directly from the amiberry emulator in retropie that is causing this. Still looking for a solution.