Thanks for clarifying! Not sure intersex is the proper medical term (it's not a stand in for hermaphrodite) but I get what you mean. I suppose the surgery scars are from that?
If it looks like he has scars, it's not intentional - maybe something weird about the lighting or the brush effects is making it look that way.
Edit: Also thanks for pointing out the language issue - I have seen the "intersex" tag used on Ao3 but it has some complicated real-world meanings and implications so I probably won't use it to describe this type of body setup in the future!