Well, Leonard's friends and interest are only university-oriented, so i can see he choose Penny, becouse she is nice(and hot) getaway to the "outer world". He really can forget about all the science stuff(although he has difficulties with it, as shown in episodes) when he's with her, and enjoy the mindless moments(in positive meaning).
I really don't view alpha male as tall, muscular man, lol. But i view him as a man with strong sense of reality, capable of snap decisions, living in abudance, and dont caring what oters think. Just watch some Sean Stephenson videos and you'll get the point. So alpha man does not mean douche, it means someone who a girl like Penny can be with, and feel like princess, becouse she subconciously/consciously knows everything will be alright, becouse a man like that can handle all situations that will occur.
Well, Leonard sometimes reveals the "man" side of him, and everytime he does i really appreciate it. But still, in their relationship, the one who looks(in terms of behaviour) like more manly is Penny. And that's why it would never work irl.