A couple of thoughts.
#1 A 30A 125V to 50A 125V cord set is not a factory made option. It is a DIY made option. Perhaps Beneteau is custom ordering them in volume but my guess is they are making them in-house.
#2 We know there is a 40A RCD/ELCI main inlet breaker but this is an oddball size, too large for 30A service / 10GA wire and small for 50A service.
#3 We need to know the wire GA, not what the manual states but actual gauge, between the inlet and the main AC panel.
#4 We need to know if the 50A inlet is 50A / 125V or 50A / 250V
#5 We need to know the size of the main double pole breaker on the AC panel, not the one near the inlet which we know is 40A.
I work on quite a few Beneteau & Jenneau boats and all I can say is they are not entirely consistent when it comes to wiring. They are also often not following ABYC standards. This makes it tough to give answers without actual critical information.
I have one Bene, a First 36.7, that had 10GA internal wiring, a 30A double pole toggle breaker on the AC panel and a Merlin Gerin C60a 40A main inlet breaker. This breaker was swapped out/replaced for a 30A breaker to pass an insurance survey as a 40A breaker is simply too big for 10AWG wire. It was much less costly to replace the breaker than the wire.. I have another 36.7 that had the same configuration but instead of the 40A main inlet breaker it had a more appropriate 32A breaker. What is installed on the vessel is much more important than what the manual suggests may be installed.