I like to think of Charlie's messy habits/dirtiness in general as an unintentional coping mechanism from growing up with his mother. I feel like it's pretty clear that she has OCD, and looking at how easily she gets upset, along with how clean her house is, I could see her possibly doing obsessive cleaning and that becoming overwhelming for Charlie. That could lead to him surrounding himself in filth, as that's his filth that he's able to control. He also shows a distaste in "gross" or "wet" things in sexual context, which could also be triggering (I feel like theres a better word for exactly what I mean but I'm not sure what) for him considering how sexual things were normalized/around him a lot as a child, both indirectly (his mom being a prostitute) and directly (uncle Jack), and he may associate sexual acts with him involved with not having control.
