By law, all compensation for services you perform is taxed the same way, it is reported on your W-2 as box 1 wages and is subject to income tax withholding as well as social security and medicare tax withholding. Your employer also pays half the social security and medicare tax behind the scenes. If your employer proposes to report salary on a W-2 and commission on a 1099-NEC, that is their way of trying to dodge/skip/avoid some of their tax responsibilities and place the entire burden of social security and medicare taxes on you. Its also illegal.
Assuming your employer follows the law and puts everything on your W-2, you will pay the same tax at the end of the year. The only difference might be the amount of withholding, this could change your refund but won't change the net amount that the IRS keeps.
