I don't think this has to do with the fact that he is a boy and she is a girl. I think that it has more to do with the fact that she is "his" baby and she is important to him.
I don't see this as abnormal, but what you should do is to redirect him to do other things. Babies should ALWAYS be supervised around children, so it is good that you are paying attention. But I don't think that it's a good idea for you to keep asking him why he does things he does. What do you expect him to say to you? He's 4. He doesn't know why he wants to pat her bottom. I kind of think that the idea of "if she is real" is probably closest to the truth as you are going to get.
Don't make her private parts sound so much like forbidden fruit either. It will make him even more curious.
The older she gets, the better, especially when she starts walking around and taking his toys. Then he'll know she's plenty real, and instead of patting her bottom, he'll be grabbing toys out of her hand and yelling "Mommy!!!"
Dawn