That reasoning I won't accept. As Khuutra likes to put it, the comic isn't part of the canon of the Metroid series or something like that.
On top of that, you have it backwards with your Batman example. The 60's show isn't the start nor the foundation of the Batman canon, it's actually in the same boat as the Metroid manga. Which means what you are trying to do here is essentially trying to convince us that the 60's Batman is the real Batman.
60's Batman created "The Bat-Tusi" dance. That makes him the definitive Batman.
And the manga may not be real canon. I don't know. Who knows what crazy shit goes on with Nintendo continuity. All I know is that when the games weren't able to portray Samus with any sort of personality, the manga was the earliest attempts to fill in the blanks. So, when Samus has post traumatic stress disorder, is obssessed with a baby Metroid, or something like that that's already been shown as part of her character, I'm willing to accept it a little more.