You are mis-applying the confusing IRS code. It says that churches automatically qualify as "tax exempt" similar to a non-profit 501(c)(3). Unless the church specifically APPLIES as a 501(c)(3) is is only a "non profit religious organization" that qualifies as tax exempt. People are misreading the code, which the IRS isn't going to complain about.
Are we really saying anything different? You are correct in saying that a church automatically qualifies as tax exempt, and this predates the establishment of the 501-C-3 part of the tax code. Churches do not have to be 501-C-3's, but many have thought they did have to do that. And the IRS cannot take away the church tax exempt status, though they threaten and scare us into thinking so.
Are we really saying anything different? You are correct in saying that a church automatically qualifies as tax exempt, and this predates the establishment of the 501-C-3 part of the tax code. Churches do not have to be 501-C-3's, but many have thought they did have to do that. And the IRS cannot take away the church tax exempt status, though they threaten and scare us into thinking so.