If you have a turret set as 'turret' set to shoot at 'missiles' docked to a turret (which will apparently force the second turret into 'ship' setting) set to shoot at 'missiles' docked to the base of the turret the following will happen:
a) The turret at the end of the chain will shoot at missiles
b) The turret in the middle of the chain (the one that sets itself to 'ship' will shoot at all targets