Mostly it’s about freedom from religion as promoted by a government entity. Both separation doctrine and free exercise pertain to the First Amendment in the US. It doesn’t forbid private citizens or entities from promoting religion in the “public sphere” which is Habermas’ concept of ideas being batted around in cafes and whatnot during the Enlightenment.

As a matter of common decency people should refrain from excessive religious expression in public, so as to not become obnoxious to others. But that’s not the same as saying they must refrain. And others have the right to ignore the religious in whatever sphere. Jesus said something about keeping prayer private (in the closet).

There’s no danger of totalitarian repression of religious expression in a secular society. There’s no necessary zero sum binary of theism vs atheism. There is a danger in theists acquiring too much political power and quashing the rights of nonbelievers or minority viewpoint believers.

References to a specific dogmatic Being, possessing an ability to defy Thou's own physical system, should not be allowed within a public sphere. References related to the nature of human experiences and processes in general are more in the realm of spiritual-philosophy as they evoke emotional and/or sensational knowledge. That would alter quite a bit of the acceptable landscape and behaviors.