There are all sorts of complex practices and laws around churches, because "religious freedom" is really a minefield. It's not that the state cares about the law, but that the narrative of the US is deeply intertwined with the narrative of "religious freedom" and "escaping religious persecution." (I probably don't need to tell anyone that the people "escaping religious persecution" were some of the absolute worst humans on the planet who were not being persecuted but wanted to be free to persecute others... but I digress.)
It is not aligning with the law that matters, nor any other sort of legal justification for their authority. Authority comes from a complex memetic fabric of woven ideas. This fabric can be attacked, these threads can be pulled out, and eventually the fabric unravels and the authority collapses.
When central authority collapses, dual power institutions pick up the pieces. They replace the faltering authority. Today, as the US government is frantically burning itself down, corporations and churches are the two most developed institutions prepared to fill that void,