Hello Ron, I have seen what you are trying to do before. On my end of things as I do RF boards things like transmission line stubs that need to be grounded at on end or shorted to ground can be a problem unless I have a real footprint for the actual transmission line.
I think it is really best to not "Hack it" if at all possible. Your schematic from a net perspective should match the board. I agree with your boss in that he does not want to allow it.
If that board ever needs an ECO I think it is highly possible that things might go bad and a board may come back without the short.
Now you could directly edit the gerber files before you send them out to the board house. I would not have the board house make any changes to the gerbers, thats kind of playing with fire.