There are many free tools can manage this. Here are two free tools for you.
As for the chapter markers preserving and file tagging, you need to try it yourself with iTunes or Handbrake. They are quite powerful and maybe can be helpful.
I have searched video audio tools for years and think you may try a detailed guide for this. Get it in google by convert mov to m4v cicever. It can handle markers and tags well there. Hope this can be helpful for you and other readers here.