The Shulchan Arukh (Y.D. 282:19) discusses stacking various sefarim. There it is stated that one should place a Chumash over other books of the Tanakh.
Suppose I have a set of Chumashim with each book of the Torah in a separate volume. Is it problematic to place Shemot on top of Bereishit, for example? In this case, all the books are part of the Chumash but they're out of the canonical order.
Related: Stacking Seforim