It may be a matter of semantics don't really think you should consider any pain "benign." Pain is an indicator that something's wrong, and if you ignore it, just chalk it up to fatigue, you're asking for trouble. Stand up and stretch, take a little break, walk around the room when you feel it. Yes, if you practice long enough, even in an ergonomically correct posture, you'll eventually get tired, but you should appreciate the difference between fatigue and pain.
“People may say I can’t sing, but no one can ever say I didn’t sing.” --Florence Foster Jenkins