Shape Flesh is... well ok in the actual rpg rules its a temporary thing, I'm making it permanent for the sake of this quest because that's much easier to keep track of. So yes, Vincenzo could make a change like that and just leave it in place. He's not going to, in this case, because he's still carrying a lot of cultural baggage about mutation and how his view of himself is tied up in his "natural" form. Adopting a more... I guess transhumanist mindset would be a reasonable description, where he's willing to just radically reshape himself over the long term, that's something he can potentially reach as the quest progresses.
(Or he could embrace Tzeentch and get right past those pesky mental roadblocks about the sanctity of the physical form)
"Useful mutation" is pretty broad. Vincenzo could indeed give himself better senses by copying those of another species. Notably, this would expand his capabilities and options, but it wouldn't be a case of "I use shape flesh to set my strength score to 10" - if you gave me hyper-swollen muscles overnight, for example, I'd probably be a right clumsy fool who still acted like I expected to be as strong as I was yesterday, rather than instantly figuring out how to move and fight with my new bodyplan. Bit of an arbitrary limit, but that's what xp spending or specifically directed plot developments are for.
