I never understood how people could use bootstrap with custom designs. It gives you CSS and JS for so many elements and classes so if you want it your way then half your CSS is just undoing (like `margin-left: 0` or `font-size: inherit`) their styles.
If the decision is to use Bootstrap then you have to design with it rather than against it.
The defaults are pretty sensible, so as long as everyone - including the designers - understand they need to customise the design to Bootstrap rather than Bootstrap to the designs it works really well.
It' a fast way of working as Bootstrap has already done most of the basic stuff, and by making changes in the right places it's easily possible to not make it look like 'just another Bootstrap site'.