I have looked back at the chapter in question—”Axioms of the Sophia Perennis” in The Transfiguration of Man—and I think the solution, though you have already said you do not find it satisfying, is simply that Schuon is writing with a western readership in mind. In fact the specific formulations that seem so problematic to your Buddhist friend may well have been culled from a letter to one of Schuon's disciples. I cannot be sure of this, but I do note that the preceding section of the chapter—beginning with the words “We say that there is an absolute, transcendent Reality”—are verbatim from “The Book of Keys”, No. 1097, “What We Say”; as I believe you know, it was not uncommon for FS to use a variety of pre-existing materials, originally prepared in answering specific questions that had been put to him by disciples and other inquirers, in composing chapters for publication.
So I strongly suspect that what we have here is a transposition of the metaphysical, and therefore universal, “axioms” of the Sophia Perennis as such into the idiom of a western exoteric tradition, a transposition that entails their reduction to a “more elementary” level, though a level that is nonetheless symbolically and sacramentally “essential” for those who subscribe to that tradition. Perhaps I am splitting hairs, but I am struck in rereading the relevant section of the chapter by the fact that while “the fundamental data of the Sophia Perennis” are said to be contained in “human intelligence” as such, the more elementary set of axioms can be adduced only with the aid of a personal pronoun: thus Schuon speaks of “our spirit”, “our Benefactor”, “our Judge”, “our soul”, and “our innate theology”—not, N.B., “our metaphysics”, since metaphysics belongs to no one and no religious collectivity.
I agree with you that the title of the chapter has a universal and principial ring about it, and given this fact one may be surprised to find that it contains certain formulations of a more “confessional” order. It is important to remember, however, that FS, metaphysician though he was—to say the least!—was also a spiritual master and that many of his writings were aimed at provoking anamnesis in what he knew would be a largely western-born or western-educated audience. If he often gave pride of place to the “saving strategems” (upayas) of the semitic religions, most notably those of Christianity and Islam, this was itself an upayic, and “pastoral”, means of his own. He was, in short, not writing to or for Buddhists. By the way he discouraged Marco Pallis from remaining in a Tibetan tradition on the grounds that only Amidism was appropriate for a western psyche; Pallis accordingly made the change.
I have copied C. on this message, as she had raised something of the same question recently in a different context. She had written: “In his reflections on Schuon that you gave to our class, Whitall Perry notes that Schuon faulted Coomaraswamy for denying the eternality of individual souls. I wonder if those who seem to differ on this issue do so primarily as proponents of varying methods: for some it is more or less helpful to think more or less about their immanent and individual self while for others it is a distraction”. In replying I observed: “It was Schuon's spiritual vocation to speak mainly to the West—and this of course in an operative and not a merely doctrinal way—and thus to make provisional use of a language that characteristically gives a greater weight to the ego.” Doubtless there is more to the difference between FS and AKC, but surely this is an important factor in explaining their differing dialects.