Sure, the Impala thinks she's a girl, but Dean knows it's his body doing those things when she takes over. What's more, he knows the Impala's history with Sam. Since your Dean is bisexual I get why he doesn't mind the former, but the latter . . . he and Sam are both kidding themselves really, if they think things are above board because her consciousness is driving their bodies. But I guess that's your point, right? These two guys are massively screwed up in a sexy way.