Melonlity, those are great points.
I think the reason we have to generalize about "all manga," though, is that racism is not treated with anything like the gravity in Japan as it is in other countries. Japan is a very, very casually racist country; they aren't violent or hateful (usually) but they think nothing of putting, say, a blackface character in a child's game.
That's the problem with Jynx, for example. You take this game aimed at children and it's so cute and fun, and then, just bam!- This insanely racist caricature is thrown in.
The problem with Japanese products is that the racism is so random and unpredictable. You take a property like Pokemon with literally hundreds of characters, and there's just that one, single insanely racist one thrown in randomly.
No, we can't talk about "all manga" but we are kind of forced to, because the racism in manga is so randomly distributed, you could find it literally anywhere, any time, and so we have to be wary of *all* manga.