I wouldn't say that last one was about school prayer, i.e. teacher lead prayer in the classroom. It was about freedom of religion in school for everyone, including teachers.
Which is how it should be.
Saying that someone is not allowed to pray falls firmly under the "preventing the free exercise there of" clause. Which, for some reason is never brought up by people on the left and very rarely by the right.
The "religion is a private matter" or "you can believe as you like just do not bring it into the public square" is Old World thinking. And it is why that clause is in there.
The Founders were of the opinion that you should be allowed to bring your religion into the public square and do so openly.