Mannerism was not popular in the Baroque era because they are both two completely different aesthetics/movements and they did not happen at the same time. Mannerism happened about a century before Rembrandt's birth and Dutch Baroque.
Also, you can't just call it Baroque because each country had its own style of painting during each of their Baroque eras. So, you have to specify which type of Baroque you are talking about. Plus, the duration of the Baroque era differs with each country.
Rembrandt was part of what we call The Dutch Golden Age or Dutch Baroque.
Also, most of his religious paintings were early in life, not later. He did less religious paintings as he aged.