A use case for manually unsubscribing is if you have an account on some site (say, an online retailer), and you don't want to run the risk that everything from them gets caught as spam, for example receipts or password resets that you do want to see.

Another is if you get signed up for multiple different streams of messages ("What's New!", "Tips to Get the Most out of X", "Company Communications", "Coupons", etc.) just by signing up for an account (and, as you point out, not actually opting in for any of them explicitly). Since Gmail does not always flag all of these different things as spam, it can be more efficient to go to the "unsubscribe" page and uncheck each of these streams yourself.