Joomla does not load bootstrap CSS automatically, but it does load the JS. If your template uses the standard method to load the Joomla head:
<jdoc:include type="head" />
It will load mootools, jquery, and bootstrap files in this order:
It does not load CSS files. You can test it by removing the line from your template file, then checking which head files go missing.
The bootstrap CSS is loaded by your template. Joomla (since 2.5 I believe) included Bootstrap 2.x in their media files for easy access. Protostar for some reason does not call bootstrap from the media files. Instead, they have copy and pasted the entire bootstrap CSS into their template.css file. Other frameworks call Bootstrap. Warp 7, for example, does have a checkbox to enable or disable Bootstrap.
Since the frontend and backend have different templates, Bootstrap can be loaded or disabled for one and not the other. There is no dependency if you wish to disable Bootstrap from the frontend and not the backend.
My preference is Bootstrap 3, so on several different custom templates, I've downloaded and included the bootstrap 3 css in my template head after the joomla head line and within my template head tags:
$document = JFactory::getDocument();
$document->setMetaData( 'viewport', 'width=device-width, initial-scale=1, minimum-scale=1' );
The method is slightly different for frameworks such as Warp 7. You can also load directly from the bootstrap CDN url if you prefer.
So Joomla does not force you to use Bootstrap or any version of Bootstrap, at least for the CSS. You could use other responsive frameworks if you like. It's all done in the template. No need for hacks or plugins.