It was to evoke BB and Snake's eyepatch in 4 obviously but the in-game reason is that they didn't have time to make a brand new cybernetic eye so the eyepatch is actually a high quality sensor superior many times to any human eye. It's like a camera wired to his optical nerves, or what's left of them. The eye Sam cut was still human.
Frank Zappa is God. Fact. King of Heroes, do you have enough swords?!
I would assume the entire body is new (since the Black body has barcodes on his forehead and such that the White body lacks), but that does beg the question as to why he was still missing an eye. Unnecessary inclusion of a bandana? Sure, I'll buy that. He looks badass with it anyway.