Samus isn't really supposed to fit traditional masculine-feminine rolls. She never has. She's always been a chick but played the protagonist role of a protector and space warrior, but under the armor and her general backround you get the idea that she's extremely intelligent(self-designed chozo spaceship, wearing the most sophisticated piece of power armor ever made by a super-intelligent and ancient intergalactic race, etc.) Basically since the start you had to realize you didn't respect her more because she was a girl but you respected more because the fact that she was a girl wasn't such a big deal.
I think this voice is a way I can satisfy my conscious in the bridge between skin-tight blonde pony-tail blue eyed samus and powersuit samus. Suitless, she caries a very feminine appearance but she still defies strict classification(even as a dominant female- neither the voice nor her outfit should give anybody but the obsessed the image of black leather or latex) by matching it with a deeper or resonant, serious, and intelligent voice. Basically, it prevents Samus from becoming too sexualized, too girly, or too masculine.