You're correct here. I see this as a - still too common[0] - lack of understanding of what classification/ontology/taxonomy is. Categories are made for humans. They're arbitrary and judged only by one thing - are they good enough for the problem being solved. In this sense, reflecting a real-life ontology in your code is usually doing things backwards - it's the code that should invent it's own ontology that's maximally convenient for the problem being solved[1]. Real-life ontologies all have their purposes, but they usually don't include making it easier for you to write software.

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[0] - Is tomato a fruit or a veggie? Is a whale a fish or a mammal? Etc. The answer to that is just "either, none, whatever - it's you who are confusing culinary, economic and genetic taxonomies".

[1] - Which is some combination of code thinking and domain thinking. It's never just purely one of them.