I don't know the specific history, but from what I can tell I agree with it being shown as is. HLR gives no indication of where a southbound pair should be. St Paul is shown on multiple unofficial sources so I have to figure this came from somewhere, but at the same time if you're headed south on Charles when you get to the end of the two way you're most logically routed the other way over to Maryland Ave (which is also shown as 139 by at least one unofficial source). So it's kind of an either/or/neither situation and leaving the centerline on Charles is the tidiest way to shrug at it.
I will add the points you suggest though.