ny - with a full length gas system, as the FAL barrel gets shorter the maker will drill a larger and larger gas port to allow enough gas into the piston before the bullet exits the barrel and pressure drops. This means a shorter, somewhat sharper impulse. The sharpness of the impulse is not much of an issue (as you say, the FAL is built tough), but the shorter impulse means that the pressure at the port becomes more critical, and firing ammo that's low pressure at that point in the bore may cause malfunctions that wouldn't happen with a 21" setup. The same result could happen with normal ammo fired in extremely cold conditions. Firing especially high pressure ammo may cause a relatively violent strike, which ideally you would adjust the gas regulator for, then resulting in marginal function if you switch back to lower pressure ammo.
Sure, it may still work in normal use, but it becomes more finicky and more prone to malfunction when conditions are at an extreme (hot, cold, high or low pressure ammo).