I think that they are two different sort of magic and intentions.
Pinocchio could only be rebuit cause he was a wooden boy and not born so they could give him a complete new start. He is now a boy, but will grow into an adult. If Pinocchio was a born boy. I think the Blue fairy couldn’t do anything about his death and they should try to bring him to Dr. Whale to try to get him back to life.
Malcolm was an adult who wanted to youth. He got youth not more. He can’t grow again to an adult. He will be a teenager and then die (or not).