With the implementation of Bootstrap into Joomla with Joomla 3.0 we implemented changes in the back end of the site to handle the Isis template. At the same time retaining the former CSS for the alternative Hathor template. There was however only rudimentary changes made to the front end which mainly revolved around the button displays which used the Bootstrap styling.
The rationale was that it was virtually impossible to know what template any given site was using, there being a number of different template frameworks available, any (and probably most) of which were being used somewhere. For that reason it was often necessary for a site to create a template override and for them to modify the overridden files as required to create their required display.