There is nothing "unethical" about a misc charge on a shop bill. 

Padding hours would be "unethical," adding a charge for shop overhead is not "unethical."  

It may tick off customers....it does this one....but that is between the customer and management and really isn't any of your damn business.

I think most decent managers would can your ass as soon as they knew you were badmouthing them behind their back.  If you disagree with management's practices, discuss it with them and explain your thoughts.  If they find merit in your postion, they may change the practices.  If they do not, on the balance, then they will not change them, but you have voiced your concerns.  You should be smart enough to realize that you probably do not see the whole picture and that there is probably a reason the manager is running the business instead of having you do it.  At this point, you should go back to doing your job and leave the manager's job for him to do.  

  Just isn't much need for so-called "help" like that.