If See the Light is always invereted, why not change the notation to be *not inverted
Because there would be hundreds (probably) of versions of See the Light from 1/16/99 to 8/7/03 (the first time it was inverted) that would then be incorrect (or that would need to be fixed) in the setlist archive. More importantly, the song was not-inverted when it was released on Deuce, which created a precedent for the "correct" way the song is played.
Furthermore (because I really have nothing else to do), since it is common practice for "jam bands" to invert songs, it is not an exception, but rather is the rule that "See the Light" be noted as such.