You could try to explain the application, maybe there are some specific solutions...
You can't really connect stick pots off-board due to the increase in resistance, so I don't think you can skip the board.
If you use the board to make the coordinates calculations then as you already mentioned, calibrations will be different so the two controllers will not match, I imagine the stick movements will just jump around.
You can manually calibrate pots to achieve 0-7% deadzone from my experience, so it would also depend on the settings of your application, if it allows for deadzone adjustment or not.