I see. Please correct me if I'm wrong - calling JHtmlBootstrap::loadCss($includeMaincss = true); is just useless then.
If the bootstrap main css, that is part of the main Joomla! 3 package (the one I'm referring to), is already a customization of the original twitter Bootstrap css file, that accommodates some JUI features, specifically the one related to the modal, using it makes no sense then, as far as I understood. Not so sure about this, but thanks for the follow up.