In practice, empowered autos are prevented from damaging turrets when Riot doesn't want the champion to be good at splitpushing. I agree that this is terribly inconsistent, and that if a champion is innately good at splitpushing, or too good at it, then that needs to be solved through gameplay changes that target the actual playstyle more consistently, not special-casing that is damaging to clarity.
What also frustrates me is that often this kind of exemption is given specifically to fighters, a DPS class that should by all rights have good pushing power, whereas marksmen, who almost all have some sort of autoattack steroid, are fully allowed to convert their own abilities into turret damage, while also generally having no other limitations to their waveclear either. At the very same time, marksmen are still excused for being mandatory under the pretense that they're supposedly the only class capable of taking turrets down properly, which to me feels like even more of a double standard. More generally, I feel many more abilities, not just empowered autos, could damage turrets and still be fine, and I'd be in favor of increasing turret health in compensation for having them take damage from abilities, particularly since it could open up interesting opportunities for artillery mages and other casters.