It doesn’t protect the ammo. There is no part of the autoloader shielding the ammunition except from above, and even then, it is easily penetrated even by secondary spall. The misconception that “the autoloader protects the ammunition” is one borne from confirmation bias.
When someone aims for the ammunition on a USSR/CN tank, but does not ignite the ammo, only destroying the autoloader, this does not necessarily mean the autoloader absorbed the hit. Instead, this means that the shot wouldn’t have ignited the ammunition anyway, even if there was no autoloader module; this is entirely possible either due to a bad shot or parts of the carousel which are empty due to the low number of shells left. Autoloader module is 100% a nerf to the tanks which it is put on.