They are. There is no difference tax-wise for a non-profit and church.
While both churches and non-profits don't pay tax, they are treated differently. Secular non-profits have to account for the money coming in and out of the organization, while churches don't have to account for the donations or expenses.
To me, reporting makes sense. For an organisation as big as a church, employing a few accountants seems like value for money simply because then fraud will be deterred.
If you argued that religion was not an intrinsic social benefit then you might start saying that some of what they do is not non-profit work. That could get interesting.
I'm not from the US, so I 100% expect those things from churches already. These sound like completely reasonable demands I would have on any public institution.
https://ffrf.org/outreach/item/14005-churches-and-political-...