I think, this is not good consideration from prestashop developers. I have same problem, actually uploaded 50k products from csv and really in category column "CATEGORIES (X,Y,Z)" means
X = DEFAULT CATEGORY, but its bad. Default category should be automatically deepest one, it means Z.
Actually i dont know, how to change on all products, because its so many and also categories and subacategories is very many.
SQL query is not effective on so many products, categories and subcategories.
How to do ?