Other manufacturers use the "half-washer" method for attaching different thickness manifolds with the same stud/bolt with perfectly fine results. The key is to either epoxy the half washer to the full washer or braze/weld it. Heck, if you have a welder you can just put some weld on and grind it back down to the appropriate size.

Going the other way (carby exhaust with FI intake) will have the same problem in reverse.

Another way to address the problem is to spot-face the area where the mounting washers sit (and cheaper).

The FI manifolds are thick because the aluminum intake manifold was cantilevered out so far (long torque arm) and the thin flange was more likely to fail.

Late CARBY engines had a separate aluminum intake manifold too that I have not measured but I believed was also thicker (as opposed to a modified Iron intake/exhaust combo which would, logically, be thinner).

Mike!