This is my take on it and I'm happy to be corrected by folk more knowledgable/ more experienced than me;
When you are rolling along the runway at speeds where the rudder is effective during a crosswind departure, you want to control your direction with your rudder while preventing the upwind wing from creating more lift than the downwind wing. If you end up in the situation where the aileron input is creating a drag towards the upwind side of the runway, then the opposite rudder you will need isn't to counter the wind, it's for the aileron/spoilers.
I have a feeling this happens quite a bit.
I think Boeings technique is designed to prevent excessive control inputs.