An exposed database you can manage/navigate with better tools like your file manager or the Everything search engine without having to launch a much less frequently used app

And not just that, it's also future-proof, so if calibre ever "dies", and you find your old backups 10, 20 years after, you'll still be able to get all the books out!

This is not true for many programs, even opensource, where data gets stored in many different obscure ways that cannot be retrieved/restored later, sometimes even if the software still exists (but is a few versions newer and doesn't recognize old formats anymore).

Mine is formatted as $AUTHOR/$BOOK_NAME/$FILES. I don't think it's very hard to navigate. If I use a find tool on that structure it can pinpoint any book, AFAICS.

Note: This is what Calibre does after I import them via its front end. No secret sauce.

You don't have too. You can actually script something out as the actual database is sqlite and the information is replicated inside each book folder.

I already have my files sorted and organised