Cedar, I am going to guess, since you say he looks much better unclothed than clothed, that it's really all about fit for him. Are you in the US?
Unless you can be more specific, I doubt he has a "strangely shaped body" .... it's probably the clothes, NOT his body. And my heart goes out to him, because for decades I thought it was something wrong with by body too. Now I realize there's nothing wrong with my body - it's the clothes. Off-the-rack clothes are cut for "average" bodies which means very few people actually fit in them.
It may be that he is simply fit and at ideal weight, but that the clothes are designed for the 70% of the market in the US who are overweight.
My DH struggles with this too: by the BMI charts, he is at ideal BMI. Our fancy electronic scale tells him he has the Body Mass of a 21 year old (and he's 45). Yet, in this society, he feels "scrawny." He's not - he's simply fit and healthy!! He bike-commutes daily and doesn't spend a minute in a gym, preferring to work his muscles in the garden and around the house lifting heavy things in the course of doing productive tasks.
It is hard for him to find clothing off-the-rack. That's one of the reasons why he has a penchant for vintage clothing (I say "vintage" but I mean clothes from the early 80s). Clothing was made smaller back then, because people were smaller. That was before the gymrat boom, and before the obesity epidemic.
Seriously... go into TJMaxx or Marshall's.... and try to find a Medium sweater or sweatshirt. The racks will be flowing with L, XL, XXL, and XXXL. Then remember that men's clothing is affected by vanity sizing too, so that Large is what used to be an XL.
I am assuming that you are in the US... if you took your SO on a getaway to europe, where people tend to be slimmer, he may come back feeling much more positive about his body. I know DH felt much better after two weeks in Paris seeing men his size and shape wearing beautifully cut dress shirts that actually fit in the shoulders and weren't loose. (Not that I can get him IN one of these shirts quite yet... but I can still wish.... )
P.s. I hope it's obvious to everyone on YLF that while I have a definite preference, I'm a firm lover of men in any and all shapes and sizes.