You're missing my point. I'm asking how and why exactly, in-story, Alphinaud came to Namai. Did we call him? Nobody ever mentions contacting him, he just springs up directly after we tried to assassinate Zenos. What made him decide to leave Kugane and come after us in the first place? The writers don't even bother to explain any of that. The reasons behind why Alphinaud stayed behind might have been more convincing if, again, he actually did anything while in Kugane that was worth mentioning later on. When Tataru stayed behind in Ishgard, back in 3.0, her actions during that time had a direct and meaningful impact on the plot, later on, with the information she gathered and the connections she made. They tried to give the same explanation for Alphinaud, but failed to provide any consequences for him staying behind, making it all look like a lazy reason to not have him along for the Ruby Sea Ride.
Also, I really do not understand how lying about your identity is an 'unimportant lie'. Maybe it's the same person, but she was still lying to us, which is generally not something that friends are supposed to do. I never said the WoL wasn't friends with Yda, but if they were friends, it'd be pretty crappy of Lyse to knowingly and directly lie to the WoL's face for however long they've known each other.
And going on from that, I'd love to see more personal consequences for Lyse masquerading as Yda for so long. Surely Yda had more friends outside of the Scions. What if one of the people who'd known her personally before her death, came to see her and found out that Lyse had been pretending to be her for over half a decade? "Upset" wouldn't even begin to describe my reaction to that if I were in that person's shoes.