Correct, Jean-Franois did not recognize "Le Patron" in the dark, and "Le Patron" either did not recognize his brother, or thought it best not to acknowledge his presence to Jean-Franois.
More Melvillean irony, like "St. Luc" listening to Beethoven.

I don't think Jean Francois recognized Luc - it was night-time and they weren't talking. I liked this scene best, especially since Jean Francois had wanted to tell Luc about his recruitment, but thought he wouldn't understand, living in his books.

You are correct. 'Le Patron' does take a separate boat, but his brother IS rowing. I couldn't figure out if the voice-over meant that J-F was saying they should discuss this moment together after the war, or if he didn't recognize him (perhaps Le Patron was disguised or his face covered) he hoped to tell Luc the story.
One other discrepancy I noticed: Philippe tells J-F to wait for 3 longs and a short of lights; but when the signal is actually sent, it was 3 shorts and a long.

Maybe I'm confused, but this is the translation I have as he rows the boat. Big Boss' back is to us, but he is obviously looking straight at the other character:
"So strange to think the big boss looks like any other man. Here in this boat, where base and tip of the pyramid meet. Strange. I'll have to talk with Saint-Luc
about it after the war."
When he rows up next to the sub Big Boss gets off and we see his face for the first time as he enters the sub.

The Big Boss went to the submarine in a separate canoe. The film highlights that part. I assume he stayed in a separate part of the submarine.