Protein is always good, but think about the point of loading up the viscera with food and THEN using the musculature. What happens is the viscera tends to shut off, meaning anything you eat immediately before exercise tends to sit there, unprocessed, until the body realises you aren't running from the lion.
And no, bodies DO absorb what they need but they also absorb a lot of crap as well - think sugars. Carbs from grains particularly are NOT something you want to be absorbing. Our bodies have systems designed to make, store and use fats, not sugars. That's why there's a diabetes epidemic on the planet.