Because that's what everyone says you're supposed to do, I don't know!
The human body distributes energy and oxygen and whatever to what needs it. You're not losing efficiency by not "taking more advantage" of upstroke muscles.
What you want to happen, is to let the huge muscles that can perform a task most efficiently perform that task. The hip flexor muscles that come into play on the upstroke aren't those muscles.
Actually, there's evidence that not only do you lose efficiency by pulling on the upstroke,
it can even reduce instantaneous power, despite it
seeming obvious that more muscles should in the short term be able to churn out more wattage. It seems that neurological limitations and/or hip stability compromise the gains.
It's not necessarily a bad idea let your hamstrings do some gentle lightening on the upstroke to smooth the form and get good ankle motion going, but this still isn't a matter of pulling on the pedals; measurements of pro cyclists show that their pedal force is still overall slightly downward on the upstroke.
For an analogy, consider a more natural motion: endurance running. After a powerful downstroke, leg momentum and body rotation does a lot of the work in putting the foot back into position for another downstroke. In this case we *do* need to use our hips a little, but not much; they're weaker muscles, and we use them only as much as the stroke requires. In the case of cycling, one leg's downstroke fully forces the opposite leg's upstroke to happen, so we sort of don't need to rely on our hips
at all to bring the foot back into position for another downstroke.
Also, overuse of hip flexors can cause lower back and hip pain.
//==================
tl;dr The idea that you should be driving the pedal all through the stroke was probably the invention of a clever clipless pedal salesperson looking for a way to upsell someone off their stock Wellgos.