Sometimes a phrase we use all the time will suddenly catch my ear and leaves me wondering where it came from and why.
this is a fairly common expression
A dictionary from 1740 defines knuckle as
knuckle or knuckle down
to stoop, bend, yield, comply with or submit to.
The allusion appears to be with the subservient gesture of stooping with one's knuckles low down or on the ground.
Somehow when I hear the expression 'knuckle under' I get a mental picture of the great apes rolling along with their knuckles on the ground.