First, a little background on the actual meaning of the song... wall of text from the Tool FAQ:

G36. What does it all mean, 46, 2, shadows?

You could write a whole FAQ for this one question alone; the major underlying principles relate to chromosomes and Jungian theory. Some of the ideas behind this song are based on the teachings of Drunvalo Melchizadek. Here's a snip of an interview with him (Leading Edge, 12/95): "There are three totally different kinds of humans on the Earth, meaning that they perceive the One reality in three different ways, interpreted differently. The first kind of human has a chromosome composition of 42+2. They comprise a unity consciousness that does not see anything outside themselves as being separate from themselves. To them, there is only one energy - one life, one beingness that moves everywhere. Anything happening anywhere is within them, as well. They are like cells in the body. They are all connected to a single consciousness that moves through all of them. These are the aboriginals in Australia. There might be a few African tribes left like this. Then, there is our level, comprising 44+2 chromosomes. We are a disharmonic level of consciousness that is used as a steppingstone from the 42+2 level to the next level, 46+2...These two additional chromosomes change everything."

Personally, I think the song title is written this way for the following reason: The proverbial "We" mentioned here (since we all have 46 chromosomes) is so fleshed out, so familiar, and that's why it's witten in long form. A part of all of our existences, as it were. Since the 2 chromosomes are unfamiliar, separate from our average existence, they're written in a different form in the song title.