Of course there's a logic to it, but something else precedes that logic -- which has to do with your interiority, be it your self-identity (the image of yourself that you have in your head) and/or your feelings.
If certain bits make you dysphoric, surgical correction is a logical choice, because for most of us that's what will make the dysphoria go away. And, on the other side of that coin, if your internal image of yourself is female, and includes having a vagina, the euphoria of getting to the other side and being "correct" in our embodiment is equally compelling.
Finally, trust your wife when she says she knows what she's getting into. She's done her research, she understands this is a distinct possibility (a probability, actually) and she says she's still staying with you? Believe her, and count your lucky stars.