If you use the .less sources in your project and compile them as part of your pipeline, you can affect bootstrap styles to a much larger degree with a much smaller set of changes. As an example, changing values in bootstrap\variables.less will propagate to all the other dependent less stylesheets.
That's the approach I took for my latest project, and was able to upgrade from 3.0.1 to 3.0.3 this morning with very few headaches.
That's the approach I took for my latest project, and was able to upgrade from 3.0.1 to 3.0.3 this morning with very few headaches.