Well, it is covered by fat. When doing it bone-pressed, you're just pushing the fat out of the way. With non-bone-pressed, you're not and are measuring on top of the layer of fat.
NBPEL can change via decreasing or increasing fat, stress, body temperature, and levels of hydration. BPEL can only change from decreases or increases in penile length caused by growth or EQ changes. Measuring the same place, same way, same EQ every time, BPEL is the only accurate way to measure gains. NBPEL is just there to know how much of your penis is showing and to compare to BPEL to know how much inner penis you have. NBPEL will always be less than BPEL.