Maybe it's because Boyd's focus on Echo is non-sexual? Yeah, Paul is worried about her, but he also wants in her pants. Boyd's just plain worried about her. That significantly lessens the creepiness factor.

It's not clear to me whether Paul was signing up to work for the Dollhouse similar to Boyd, or whether he was signing up to become an Active. I'm not sure if I missed something, or if it was left ambiguous on purpose.