Obviously Franck's compositions were original, and not based on hymn tunes, a la Bach. As to where the 'chorales' are, what would you do with maybe the most famous example, Elgar's "Enigma Variations"?
Somehow, in No. 2, I've always considered the opening pedal theme to be the chorale. Why else would it be so prominent in the piece? In No. 1, I agree it's the Vox Humana theme, and in No. 3, the soft part that comes in after the beginning preoration. What is interesting is his treatment of those themes as the music progresses, in each case eventually winding up as a full-organ treatment at the end.
In No. 2, Marie-Claire Alain calls that Vox Humana part a "seraphic theme", which, of course, closes the piece. But it's always interesting how various performers analyze a piece of music. Who knows how close they are to out-guessing the composer? And, did the composers themselves spend so much time analyzing? That's mostly for people getting Ph.D.'s.