A scanner glass is quite rigid. I made the tray the width of the scanner glass to maximize the size of slab scanned but even if I hadn't the weight is so lite. you could probably put a gold bar on the glass and it wouldn't affect the optics. You would have to have a HUGE sheet of glass (feet square) and even then the flex would be so slight. Also the scanner has a wider focal distance than you think, even at a very narrow focal plane it would still have enough even if there could be flex which again there won't be.
BTW why are you going this route? I did this so long ago only because digital cameras hadn't been invented yet. The resolution difference between a scanner and a camera is MASSIVE and you are not shooting through a sheet of non optic glass like you are in a scanner.
If you have seen Pat McMahons book he shot those pictures using a camera above a tray filled with fluid and the flashes on either side to not create reflections and look at the quality of those pictures. The specimens don't have to be polished due to being immersed in the fluid. The only issue as anyone who has tried photographing slabs web is not matter how many times you have cleaned them the always seem to shed some junk which means you are changing the fluid quite often to keep a clean environment for the photos.