At a certain point, I'm just 'pulling the chain' in regards to 'measuring protein'. If it were my operation, I'd want all the data I could get. That includes yield, soil type, water retention, etc. etc. Measuring what is produced is essential in good feedback control for your input variables. Amount of available nitrogen directly affects kernel protein as demonstrated by much research. To control nitrogen input, it only makes sense to measure the nitrogen bearing product in the harvest.

The uptake of protein into the kernel is definitely affected by nature for dry land conditions, and is non-linear.
(from http://www.usask.ca/agriculture/plantsci/winter_cereals/imgs/chapt08/proteinconcentration.gif)