They are on the ship in the Limsa intro (started as an Arcanist), and they slept right through the pirate attack that occurred there. You can even see the twins still asleep for a brief moment after your character and the merchant head back below decks.
Considering it’s implied this was the point where the twins had first arrived in Eorzea, this means you were seeing them at the end of what was likely a very long journey from Sharlaya. Can’t really blame them for dead tired.
I just re-watched that part, and I got the impression that he was actually making a joke...
And I'm willing to bet that's not what he said in the Japanese version, additionally. One translator I read says the English script has a tendency to write 'unnecessary jabs' at Alphinaud. Said translator talks about it here, along with translations of a couple 2.55 quests. I recommend giving it a read, it kinda shows the English script added more of an 'arrogant prick' edge to Alphinaud then was present in the Japanese script.
I think he’s learned humility. After Riol and the other Crystal Braves loyal to him make it clear they’re sticking around even despite the Braves’ dissolution, Alphinaud says this:
“My grandfather used to say that one could measure a man by the constancy of his comrades... Mayhap I am the exception which proves the rule. Nay, do not protest. I know that I am not worthy of their loyalty, Forename...
...But as Thaliak is my witness, I shall do everything in my power to earn it.”