Your not shooting flat paper, your shooting a negative which can often be anything but flat.
An enlarger is really a macro camera with the negative as a subject and the paper in place of the film.
as with most macro shots, the depth of field at the subject (in this case, the negative) is very small.
By stopping down a bit (usually a couple of stops) you get a bit more depth of field which can compensate for a bit of curl or bowing of the negative.
At the paper, the aperture controls the depth of focus. This is not as critical as it is at the negative stage but again, a bit of stopping down allows for some non-flatness in the paper (quite a lot actually).
Steve.