Good question.
Until we get something official, here's my idea:
Precise Bomb hints to me that the alchemis is putting a spin on the bomb, or hurling it so it hits at an angle. Anyone who has ever played with water baloons, or mabe even splashed his friends by stomping in a puddle on the sidewalk, can possibly relate to using angles to adjust where the splash will go.
Now assuming the alchemist is silled enough to choose the angle correctly (and Precise Bomb gives no chance of failure), then missing with his throw means the angle remains more or less the same but the target square changes.
Imagine this is a 5x3 grid of game squares.
1 2 3 4 5
6 7 8 9 0
a b c d e
So let's say the alchemist designates that he is throwing at square 8 and using Precise Bomb to avoid splashing his friends who are standing on c and d. This means he is protecting the square straight back from the target and back-right from the target. But he misses his throw and the bomb lands on square 9 instead. It still protects straight back and back-right, but now those two squares are d and e, which means the ally standing on c is not protected from the splash.
Wow, reading that it looks complicated, but in my head it's really simple: The alchemist is not designating safe squares. Instead he's designating safe directions. A square lying in a certain direction from the target is either safe or it isn't. If the throw is a miss, then the bomb hits a different target, but the safe and unsafe directions remain the same.
That gets really hard to keep track of, for simplicity I'd say he is able to designate squares and is skilled enough to make sure those squares, even if he misses, are not hit.
This very question for my alchemist prompted us to note in the print version of the APG that if the bomb misses, this discovery has no effect (there are no safe squares for a miss bomb).