I feel like the tone of “There is NO option to opt out of this unit, it is required for all students to complete” along with “As as science class we will only focus on the scientific theory and evidence.” is suggesting that their religious beliefs are irrelevant when it comes to science, which is far from an apology.

Imagine if you saw an ice-cream stand with a sign saying “The price is 5$/cone. There is NO option to eat icecream without paying. We are aware that there are many cultural and political beliefs on economics. As a capitalist stall, we ONLY provide icecream in exchange for money. We are not trying to change your beliefs, but introducing what our standpoint is.”. If you saw that sign, I imagine you wouldn’t think “ah, what a totally normal shop”, you’d think “oh boy, Something Happened Here”.

This email is proactively defensive in the same way. In a saner world, this email would be way shorter or wouldn’t exist at all, because you wouldn’t need to specify that a particular unit is non-optional, etc. Your screenshot makes me think of USA as more weirdly religious, not less.