Hi,
If you consider the categories/products/variants hierarchy as a kind of filter it should make more sense. If categories would be inherited automatically the base products and their variants would end up at the same level which might be overwhelming depending on the kind of products in stock.
Ultimately it most likely was a choice made for a particular kind of use case. Had a different one been anticipated, this choice might have been made differently. But in the end neither one is obviously right or wrong. Maybe it would be sensible to have a switch to choose the default behaviour, so if it really bugs you, feel free to submit an issue (or start coding yourself…)
