1) Religion has a legitimate place in the public sphere. Governments can support religious institutions if there are reliable criteria for administering tasks and evaluating goals. The interpretation of the freedom of religion clause primarily refers to establishing the supremacy of particular religions.
2) Religions should be open to public critique especially by people who do not identify with a religious community. Religious books like the Bible or the Koran may be read, but they may also be freely critiqued, satirized, ignored and altered by individuals.
3) Bureaucracies have no comprehension of religious or supernatural claims, and must be agnostic about any claims regarding holiness or miracles. It's sole criteria is social utility. In short, the bureaucrat ensures everyone plays by the same rules.