If it were me, I'd take the full estimate amount for the repair (the cheaper one). The guy is willing to pay for the damage he caused, which is good of him. My thinking is you might decide to go ahead and get it fixed in a week, month or year from now and if you've only gotten the tire cost from him, we'll then your stuffed.
He caused the damage. He's willing to make it right. Seems ethical to me.
Unless you are
fully certain that you will never get that fender fixed. If that's the case, then I feel you'd be doing the right thing by only charging him for any accident-related repairs you
do have done.
Never know when you might decide to have it repaired properly.
Just my humble two cents -- your results may vary