I do think that this is a creative idea, but if Brian was not a supermutant, he would never have survived the trip out to his cave. It could be explained that he got some of the supermutant benefits from the experimental serum (like the vastly increase resistance to radiation and regeneration) without getting the huge green mutant appearance. The serum could be affecting his brain and making him think he looks like a supermutant (i.e. him imagining huge green hands instead of normal human hands). His delusions might also be caused by a psychological break from reality as a result of his guilt, or maybe some mixture of the two.
Well, he could have survived the trip I suppose hypothetically. The Children of Atom live in the crater of one of the bombs itself. I mean, he'll die eventually but I don't think the radiation itself is outrageously lethal.
Regardless, I agree with you that this turns Virgil into a much more... nuanced character xD
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In vanilla there's an aviator cap in his lab by his bed. There's a mod now that allows the aviator cap to be worn by humans:
https://www.nexusmods.com/fallout4/mods/59888
He could be wearing one when you first meet him, then remove it from his head after he's "cured".
Anyway, interesting story idea.
Regardless, I agree with you that this turns Virgil into a much more... nuanced character xD