I just had a discussion with @MrTango about this yesterday I have the same "problem" with how Barceloneta works with Bootstrap. What I usually do when theming for Plone is to separate front end and backend:
<?xml version="1.0" encoding="UTF-8"?>
<rules xmlns="http://namespaces.plone.org/diazo"
xmlns:css="http://namespaces.plone.org/diazo/css"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:xi="http://www.w3.org/2001/XInclude">
<!-- Include my.theme for front end theming. -->
<rules css:if-content="body.viewpermission-view, body.viewpermission-none">
<!-- Use the theme template from index.html. -->
<theme href="index.html" />
<notheme css:if-not-content="#visual-portal-wrapper" />
<!-- Add your front end rules here. -->
<xi:include href="++theme++my.theme/rules/core.xml" />
</rules>
<!-- Include barceloneta's backend.xml for backend theming. -->
<rules css:if-not-content="body.viewpermission-view, body.viewpermission-none">
<xi:include href="++theme++barceloneta/backend.xml"><xi:fallback /></xi:include>
</rules>
</rules>
This way the (public) front end is styled with your theme, and as soon as you enter site setup, folder contents or edit views, barceloneta is used. As you can see it is all done with view permission checks, so you can adjust it to your needs.