I've read he was, in some sense. Nevertheless his language in the 1970s is replete with ideas which are "spiritual." Look at this:
This sort of thing may have been sincere, it may have been public relations, it was the time of hippies, the age of Aquarius, all of that. Anyway, what I really want to say is that the communist-materialist understanding of Xenakis prima facie doesn't fit what we know about him in the 1970s, the period of the site specific multi-media spectacles.
Have you heard of the "world polytope?"
I know
exactly what you mean. His interests in Greek mythology, Homer's Odyssey, Plato, Noh music/theatre, Ritual, primitivism (raw, transgressive, uncompromising expression) and the cosmic etc, definitely shows strong spiritual subtext to what his music is getting at.
It's hard to put into words, but when you really experience it - you know (and feel) it! (regardless of your own religious or non-religious stance)
Something outside of just religion too, certain aspects of both the human experience (like 'fight or flight', in our animalistic layer of humanity) to mystical experiences (regardless of the origin, even drug trips are valid), to pain, suffering, joy, ecstasy.
Whether it's apparent on the surface to the average classical listener who happens to click on a Xenakis video or not, these things are inherently the foundation of Xenakis' mature musical language and expression.
The early period (not pre-Metastasis) is more preoccupied with architecture and post-Futuristic/Scientific ventures, which is where many listeners get completely lost (or put off) with Xenakis. Graphs, maps, diagrams and the sort are fixations in this period, as it is part of the journey from the naive innovator to the relentless genius.
The aesthetics of Xenakis' music (and a lot of other milestone composers like Stockhausen, who is fixated with space, God, meditation and other things), I generally don't think are things that many of the anti-Xenakis people are either interested in or are acquainted with.
The spiritualism and mysticism is definitely there, even though Xenakis himself claimed he was an atheist.
It does, however hint at the immense power that many of the ancient myths have and the truths about humanity the preserve. Confronting? Depends on the individual. Xenakis' music has an incredibly strong emotional impact on me but I can easily listen to his work on a casual basis (lol, like at the supermarket

)
Yeah, there is my informed observation on what you hinted at (a while ago)