Well I guess they want to show, that thex are so in love (or heat, at least some), they want to rush into it. So no time to get rid of the clothes. So only the necessary parts are removed. And most BL are into the "the bottom has sensitive nipples", so they have to remove the shirt for them too.
And I guess some mangaka are just more confident in drawing clothes, than body parts. Because muscles and joints look different with different positions and if you don't have someone modeling for you, it can look off easily. While clothes are easier, not only can everyone imagine it easily, farbic has a certain way it folds/falls, so you would instantly recognize if something was odd and can easily change it. Body parts are harder to imagine. Don't know how often I read comments on how weird some positions/body parts looked in some works.
Why do they always wear clothes during sex but sleep nacked? That makes no sense and ist always very strange to see someone having sex while wearing pants...
Is wearing clothes while sex a cultural thing? Or an BL thing? Because mostly the buttom is (nearly) nacked but the top is sometimes even in full clothing. Why? I don't geht it.