(The following are all screenshots taken at exactly the point described.)
I am scrolled down on the main page of http://meta.discourse.org viewing topics.
http://i.imgur.com/dr0V0dn.png
I click on the topic "Development on Windows". (My read position was already at the bottom of the topic, so that's where I go. There are no new replies to read.)
http://i.imgur.com/OMcKAW5.png
I then click the back button, and go...
http://i.imgur.com/5e4DpK4.png
back to exactly the position, the very same position by pixel, I was at.
Maybe I don't understand what you are talking about, because I can't reproduce it? Can you share some screenshots?
It is true that when you deep-link into a topic you've already read, with new replies, we take you to the top of the post you had a last read position at. But that seems unavoidable and correct to me. (You could argue we should start you at the post below the last one you read, I guess.)