Patrick, I believe that is the best photo of the windshield available (I assume from the National Archives). I did a Powerpoint 180 flip to match up to the Limo photo from 1963 (which I assume is what we see on the right side panel) - and also changed the angle on the Archives photo to try to match them up... There seem to be enough characteristics to say they are the same windshield, in my opinion.
As Royell commented, neither of these seems to have a bullet hole (at least not one the size of a pencil or so). There does seem to be some material chipped off, which appears to be on the inside, suggesting to me that whatever struck the windshield likely came from the outside... Of course, a glass expert would need to examine and confirm..
Jake, by flipping the NARA image and placing it next to the White house garage photo, you have done one great thing, proved that the damage was OUTSIDE!!! You can clearly see the depth of the lines. Damage and cracks were on the outside glass layer of the windshield. When there is a crack on the three layer windshield, crack is usually on one glass layer, does not transfer to both glass layers and this was the casa with the Lincoln windshield. Crack lines are only on the outside glass layer.