For panel enclosures, I always specify that they do not have any knockouts. I much prefer to put the holes where I actually want them and not have to deal with the prepunched ones that really don't match up with any of the standard installation methods.
The code only applies to T&M work....it does not apply to contract work.
We have in the past ordered KO's only on one end of the panel so you could use it either with or without KO's by flipping it over which gives some flexibility depending on the installation.
All responses based on the 2014 NEC unless otherwise noted