M249's do not use a Version 3 gearbox. M249's have there own independent gearbox, and I think it goes the same way for the M60's.
However...they normally accept parts for other guns making them still viable for upgrading, almost all guns use the same size cylinder, piston, and piston head, most guns use V2/3 gear sets. There are few exceptions like the PSG-1, SR-25, Famas, etc...