Does a defendant get the opportunity to question the estimate of damage supplied by the alleged victim in a criminal mischief felony charge?

Yes, it is called a restitution hearing. There are time limits to request one - usually a short time after the restitution amount is imposed. You may need your own estimate. Get the estimate from the owner, have it reviewed by a reputable repair shop. Photos might help. Both should be in the DA case file called discovery. I have seen folks pad their restitution requests.