That makes a lot of sense to me, yeah
I think you've correctly identified the source of the problem, too, in that the characterization that MC has been given is too easy to miss. I don't think it's because it's too subtle, it's because it's camouflaged. Things that you've cited as character choices are phrased and presented in a way where they could be plausibly interpreted as excuses for the self-insert blank slate: we see the MC is thoughtful and methodical, we know a character would need to be that to always let the player explore as much as they want, and therefore we assume this is a gameplay decision that the narrative is rationalizing and not an actual trait the character has. He's inquisitive, and because a character would have to be inquisitive to dig into Kota's past, or ask for all the explanations of how the research and exploration systems work, we therefore assume that's why he's inquisitive. Because of the genre of the story, and the form it's told in, it doesn't occur to us to think of these traits as more than a storytelling convenience.
I do think the best solution is to just be less ambiguous about the characterization that's already there. Subtlety is good, I'm a fan of it, but because this subtly is being masked behind what looks like game structure, and the expectations thereof, we don't even notice it's there at all.