I assume what you mean by easy familiarity is how casual they are about nudity. They aren't looking at another person who is nude, they are looking at themselves. They've seen it all before.

In the shower scene, Scully does her best to ignore her penis, but once she takes it in hand, perhaps the "dick brain" has taken over? Also, they both note several times that there is some kind of body memory, some residual of the other personality, that proceeds on autopilot when necessary. Plus, they both know how to operate the equipment, so to speak. They've both seen each other naked. I was more distressed by Mulder's idea of what proper work attire was for his woman-body. He would never leave the house wearing flip-flops in his body, why would he would he in Scully's? I decided to chalk it up to his hatred of her high heels. Plus, he is getting a voyeuristic pleasure out of looking at Scully's boobs in that teeshirt. "I look hot." Paramasturbatory, indeed.