This is how I see it. NwoD is better than OWoD in that its various splats actually work off the same ruleset, so you can include them in one story without severe houserules, but they're not actually supposed to, narrative-wise, go out drinking together the way a D&D party is meant to, so inter-splat power balance (compared to inter-splat rules compatibility) is not even a remote concern. At best, it's a warning for antagonists - a mage is going to need to be handled carefully to be an BBEG versus vampires.