I posted this together with a screenshot @ stackoverflow as
http://stackoverflow.com/questions/37024906/openntf-debugtoolbar-ui-is-overridden-by-extlibs-bootstrap3-theme

Here's the short version: the left coloumn cells of the tables inside the opened toolbar are assigned a style class “label” which unfortunately conflicts with a .label selector within bootstrap.css.
Currently I solved this by wrapping the toolbar into a customControl container, then applying my own custom css file to the container like this:

div.dBar table.grid td.label{display:table-cell;}

I feel that this should be addressed inside the toolbar code itself, ideally by changing the td's class attribute to something more specific than just “label”.

PS: great tool, btw. I use it quite regularly in most of my projects. Thanks to Mark and all other contributors!