For IP 54, jacks, keyboard, LCD screen, speaker etc., must have an equivalent of a gasket seal and exposed surfaces are themselves water resistant. Its "resistant" because its 'water proof' only under certain conditions.
The water resistance in this case is just the equivalent of spraying this device 360 degrees at 10L/min at atmospheric pressure, not submersion underwater. I would presume the charging female jack has a cut off switch so the inputs are disconnected until a male jack is inserted into it. IP54 is the least protection for using a device in the rain or marine environments, such as boats.
The conformal coating protects PCB and its components against moisture [ such as high humidity in a ship], dust, mold and other contaminants but most are not specifically designed to be immersed in standing water, the casing should do that. Coating are not as easy to guarantee as a protective chassis, which can be easily be rated for true submersion in water for unlimited duration at a specified depth.
http://www.procoatus.com/faq.html#conformal-coatings-protect-against