Non--browser-integrated password managers with 2-factor authentication are one of the best security solutions around right now. Every step away from that costs you security, but probably is still a good ways better than using passwords alone purely from memory.
Why NON--browser-integrated? What's wrong with the one integrated in the browser?
If instead you mean "browser-integrated" as in the default "remember my password", well, those are not what this paper discusses and are generally better, though they are still not as desirable as a standalone less-privileged manager.
The idea that the password manager should be separate is practically common sense. Browsers provide more surface are for attack. Browsers are made to share content and work with network data. Ideally, your password manager should never touch the network ever. It has no need to.