I myself have no horse in this race, because I have no issues writing scripts to warp upstreams divergence into whatever shape I prefer locally. But....this seems like the sort of thing a bash script could fabricate by way of symlinks for anyone who desired to browse it in such a fashion, whereas the reversal does not have such a programmatic solution. (Because a reverse map of this would become maintenance overhead) And symlinks exist in NTFS as well, so such a solution is not Linux specific.
However, I do like monsters categories. I guess the real issue I have with the current system is sometimes monsters belong to more than one category, and the hierarchical nature of common filesystem will never do such things justice.
If you are going to do this, I propose the creation of a category tag container element for monsters, to facilitate a tagged monster browser. Those who don't care would simply be able to ignore the tag, as it would be completely optional.