I ran into the same problem with netflix too. I have yet to figure out a solution though be interested if someone does

On my harmony smart control if I click the Menu button it takes me back to the homescreen, even in the netflix app.

The current Netflix app functions the same way on all devices if you exit the app by backing out. It opens the menu and you have to select the option to quit.

This isn't a Mi Box or Harmony issue, it's a Netflix "feature".

Just press the "home" button on your remote then ? Don't understand your question. Netflix just works this way on the Shield TV too, that's not the remote's fault, just the weird Netflix app.