Sort of. Each book is usually it’s own self-contained story (the exception being book #2 which is a direct sequel to #1) but many books follow up on characters that were introduced in previous books. You don’t have to have read any of the previous books to understand the story you picked up, but there’s some continuity and references if you have. It’s kind of like several different novel series all set in the same shared universe rather than a true anthology though.
If anything was going to get Newton in trouble with the Church, it would have been his lifelong obsession with alchemy, not his three laws.