If Churches only understood they are not required to get 501(c)(3) status to enjoy being a tex exempt entity they could avoid these hassles. The IRS code and booklets state this, but accountants and MBA’s convince churches otherwise because they like to have a piece of paper which clearly states their tax exempt status. But Churches are automatically tax-exempt under the law.
You are correct.
Still, the IR laws that establish 501(c)(3) orgs are a violation of the 1st Amendment. Congress is forbidden by the 1st Amendment from passing any law that restricts speech or the free exercise of religion. They should have been stricken many years ago.