Hadn't heard of this book, I'll have to check it out. It vaguely reminds of something Dostoevsky's Underground Man might have said when he was railing against the utopian rationalists.
It does help if you have some knowledge of the ways of the Catholic Church when reading the novel. I don't think I could have fully appreciated the richness of "Canticle" if I'd read it at a younger age when I'd had no experience with the Church. But I'll also say that it's one of those books that I love but don't reread too often since it always leaves such an impression.
But yes, I would say that the dangers of pure rationalism (without the wisdom to temper it) is something of a theme throughout "Canticle".