>>4384113>lack of menstruationsI never noticed this. Probably because it was explained indirectly when the red was having them.
On "Why?". Manga had Rei taking pills. Either to keep her stable until the time was right for Third Impact or to keep Her body from breaking up. Melanin in Her skin was absent and the rest of differences that you pointed out. And EoE had a scene of Her arm falling off. Showing signs of decay. Gendo paid the price. A tense moment. Followed by relief.
Rei's "Birth" wasn't normal nor natural. She was literally born in a tube.