I'd like to think they preserved her scalp / kept it in circulation and returned it to its position, but I have no idea if skin can be kept alive across this surface. Maybe that's what those holes in the printed piece are about, though? Or are you concerned that even with skin on top it'd alter the appearance due to different subsurface scattering?
Yeah, I'd be incredibly shocked if they didn't preserve the scalp.
On the other hand, if she did have an exposed skull, I think there's like half a century or more of media which says you pretty much have to leave it transparent. You can always wear a wig or a baseball cap, but how else will people know you as an incredible (evil) super-genius without the exposed brain?
Neither she nor anybody else is going to routinely see her skull, so I don't understand why you think it would make her feel abnormal any more than an opaque one would.
Edit: Some additional info (note the English captions): https://www.youtube.com/watch?v=IXcz3OdHSHk