I use Savarez Corum/Alliance carbon strings on the guitar I built myself. They work fantastic for that guitar. And I chose these for a very specific reason, namely the placement of my bridge and the length from the nut to saddle. I had trouble getting right intonation with nylon strings.
I did some research on this a couple of years ago when I had difficulties with intonation and nylon strings and found information about this elsewhere on this forum. I don't remember all the details but here is the core of it as I remember it, and someone please correct me if I am wrong.
As you are probably aware the string length of classical guitar is normally 650mm. To accommodate for pressing down the string the length from nut to saddle block (actual string length) is made slightly longer. And here there are many opinions on this field so I won't go into detail or discussion about what is right. But for this purpose lets say it you make the length 652mm. Then intonation is adjusted for individual strings filing the saddle block. Now, carbon strings have significantly higher density than nylon and requires less adjustments from the 650mm length than nylon. And therefore as your luthier friend pointed out, the guitar needs to be setup differently.
So, to make a long story short. It is my experience that carbon strings require different intonation and setup than nylon.
I am guessing the luthier is building your new guitar with that in mind since he uses carbon on all his guitars, so I wouldn't be worried