Yeah, it seems to basically follow Mass Ave from Harvard to Porter which makes perfect sense. (There's some one-way funkiness on the surface street--Boston/Cambridge, what can you say?) But given that the Hardware Square station existed at the time of the Red Line extension, I'm not sure why you would go under Harvard Yard. I'm willing to believe that Harvard Square station could have been located differently in a way that didn't require such a dogleg approaching Harvard Yard but that decision happened a very long time ago.