Hi Jesse,
This editor is only there to do things TTW, quick and dirty in my opinion. And therefor it's perfectly fine. For more advanced theming I always use the filesystem approach with all the tools I need and like (grunt, less/compass compiler, browsersync, ...; see the new theming training docs for example: https://training.plone.org/5/theming/theme-package.html)
You can use Barceloneta for backend and your theme for frontend only, see https://training.plone.org/5/theming/theme-package-2.html#unthemed-backend.
I see this as a problem as well and will discuss it at the conference in Barcelona next week.
My themes are almost always Bootstrap based, and usually I do something like this:
<!-- Add Bootstrap stylesheet. -->
<before css:theme-children="html head">
<link rel="stylesheet" href="{$portal_url}/++theme++mytheme/assets/libraries/bootstrap3/css/bootstrap.min.css?v={$theme_version}" type="text/css" />
</before>
<!-- Add theme base CSS. -->
<after css:theme-children="html head">
<link rel="stylesheet" href="{$portal_url}/++theme++mytheme/assets/css/theme.css?v={$theme_version}" type="text/css" />
</after>
<!-- Add selected theme color option from spirit.plone.theming. -->
<after css:theme-children="html head" css:if-content="#PLONE_THEMING_COLOR_OPTION">
<link rel="stylesheet" href="{$portal_url}/++theme++mytheme/assets/css/theme-{$color}.css?v={$theme_version}" type="text/css" />
</after>
<!-- Add default theme color in case we have no option. -->
<after css:theme-children="html head" css:if-not-content="#PLONE_THEMING_COLOR_OPTION">
<link rel="stylesheet" href="{$portal_url}/++theme++mytheme/assets/css/theme-blue.css?v={$theme_version}" type="text/css" />
</after>
<after css:theme-children="html body">
<!-- Bootstrap JS local fallback -->
<script>if(typeof($.fn.modal) === 'undefined') {document.write(unescape('%3Cscript src="++theme++mytheme/assets/libraries/bootstrap3/js/bootstrap.min.js"%3E%3C/script%3E'))}</script>
<!-- Add custom JavaScript. -->
<script src="{$portal_url}/++theme++mytheme/static/main.js?v={$theme_version}"></script>
</after>
I add the Bootstrap CSS and JS, if not already there, using diazo.
I also use the Plone Theming Extension I wrote some time ago to make it easier for integrators/end users to customize their theme (I think the advanced theming options are too complicated and can break your theme when used wrong).