Are PE input and PE output really isolated ?
Yes they are (or should be! if all is good). Voltage measurements from input to output while wired to the yachts systems will then include stray voltages from the input PE to actual ground potential. Also series resistance of the grounding system.
The 363V reading is the 118V input (Ni ) plus the 244v L out voltages. You are measuring from the -180Phase L2 (in this case wire is the “neutral” wire) to the output 244 In phase volts. PE-s are effectively coupled together by the water and grounding systems(0v top reading). The out of phase voltages add.
No, it’s best to leave the PE input terminated in the PE input connector. This secures the wire from wandering around, and it is effectively isolated / insulated.
Your 2 pole breakers and residual current circuit breaker together give the function of an RCBO, which opens both poles either on over current or ground leakage. So that’s ok.
BTW in case you missed this, the PE out is connected to N out by the J5-J7 link.