Charles Earle Funk’s book “A Hog on Ice & Other Curious Expressions” explains that long in the past the knuckle was the knee or elbow. “Thus ‘to knuckle under,’ meaning to submit to—or acknowledge oneself defeated by—another, carries back to the time when one knelt before one’s conqueror in token of submission…” I think references in other sources to putting the knuckles of the hands on the ground as you kneel in front of the conqueror make less sense.