In the case of back pain, the anatomical findings would be things like structural problems and changes with the spine, discs, nerves, tissues ect...
Clinical presentation refers to typical physical signs or symptoms that are associate with a particular disease, pain, numbness, inability to walk, things like that.
So the statement can mean that after look at the damage or disease in this person's back, their symptoms (pain, whatever) is not as severe as it could be or should be.
Of course the person could have a very high tolerance to pain too, that's my thought. This isn't something you hear Doctors say too often, its usually the other way around.
Take Care
My understanding is that a clinical presentation is how you are feeling, your pain, and the physical assessment that he did. I believe that anatomcial findings are more of your x-rays, MRI's, etc. I think that what he means by that is the actual "injury" is more severe than what he saw in the clinic just from talking to you.