I will bow to your knowledge on the automatic status of a church. However, being automatically considered a 501 (c) does not exempt the organizations from the requirements of being a 501 (c). So while I will accept your statement they need not apply for that status, that does not mean they can't lose that status.
That being said, I find it interesting that this does not seem to happen - despite the alleged war on religion.
Thanks; I have made a living for 34 years representing taxpayers, including a few dozen 501(c)(3)'s and at least one 501 (c)(4) that got one of the first letters in 2009.
There is a strict procedure in the Internal Revenue Manual for auditing or examining a church regarding its activities and tax exempt status, requiring Asst Commissioner approval before initiating any inquiry. The determination of the status of a church is a matter of the facts and circumstances. I've had four or five cases where a client was asked to provide information relevant to such a determination.
In brief, an entity is considered a church only if it has the badges or earmarks of a church. These include association with other religious entities such as theological seminaries, a statement of religious principles, standards for who can perform sacerdotal functions, a definition of membership, and so forth. The IRS can only request information on the existence of these badges, not as to the content of them. It's a fine line. The intent is to weed out obvious "churches" that are simply tax avoidance schemes masquerading as a church.