Because it is not necessary to learn PHP/MySQL. And if you add JS, even worst, don't use bootstrap at all. Don't use any PHP framework too at this stage.

It's a framework that makes things look decent enough by default though.

If your goal is to learn something other than web design (eg. PHP / MySQL), then surely you want something that can do things well in that department by default so you don't have to mess around with it too much?

That was my intention: Learning the practical side of PHP and MySQL, without having to deal with too much design and markup. At the same time I didn't want my project to like a POS, which is the main reason I used Bootstrap.