Different scenario but similar results. A coworker told me a few times in the past months, "Youre the man, dont let anyone tell you different." Obviously, not THE man, but I have good morals and a good human being, hes saying it to me because he respects me even if others may disagree IN HIS MIND.
Now this guy, he is IN MY OPINION, saying you are beautiful but he thinks you have low self esteem and may think others wont hold the same opinion...
Its a 75% compliment and 25% backwards.
When a guy thinks you are pretty... He will just say so I think.