QueryBuilder highly depends on Bootstrap components, especially buttons and icons, but you can easilly remove this dependencies with some CSS and extra config.
First you need to change the icon sets for new ones, let's say Fontawesome:
And then you need a bunch of CSS rules to mimic Bootstrap buttons (the colors set is for the default QueryBuilder theme, you will need to change them to use the dark theme).
And you are done, you can remove the Bootstrap CSS. Of course every BT based plugins won't work correctly.