Yes, you are correct to assume he's using superglue. (For sure, titebond, or other wood glues won't go through those tiny microtips/pipettes and they won't penetrate that crack).
You are also correct that with the 2pc top and 3pc back the joints won't line up and it's not worth it/appropriate to put clamping pressure on it.
It sounds like he knows what he's doing and you'll end up with a well repaired instrument when he's through.
Like I said, I wouldn't have gone to all the trouble/time/expense associated with this guitar, but if it pleases you, especially if this is a model you've really wanted for some time, then kudos to you. I hope it will bring you much joy.