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For those of you who already have existing input profiles and do not want to risk losing these profiles when trying out defaults, I would suggest backing it could be a good idea to back up your existing profile. You can do this by scrolling to the very bottom of the Controls submenu of the Options menu and activating "Save Profile" to save your existing profile. You can later load that profile to restore to an input state that you are reasonably satisfied with.
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With automatic target selection on, targets that are directly in front of your ship are automatically selected. In 3D mode, this automatically selects what you look at. The default joystick profiles were designed with this setting active, but with since buttons are also mapped to select other methods of selecting targets, this can be safely turned off.
If automatic target selection is on, it is useful to have a control mapped to "Toggle Target Lock". This locks your currently selected target so that looking at, or facing, other targets does not change your selection. Toggle target lock again to allow you to switch targets via automatic selection again.