please, update first to 3.3 and make sure you've taken in account those points:
https://manual.limesurvey.org/New_Template_System_in_LS3.x#FAQ_about_theme_customization

I am running 3.3.1+180214 and did follow the FAQ. The problem is that custom.css is never loaded in the HTML code. In the theme editor preview the custom.css is loaded but on the actual HTML in a survey it is never referenced nor used.

could please try to uninstall and reinstall the theme from theme list?

Thanks, reinstalling did enable custom.css. However, when I change the variant to Sunset_Orange, custom.css is no longer use. The problem is that the files_css column of the lime_template_configuration table originally says:

{"add":["css\/ajaxify.css","css\/animate.css","css\/variations\/sea_green.css","css\/theme.css","css\/custom.css"]}

after selecting Sunset_Orange it says:

{"add":["css/animate.css","css/ajaxify.css","css/variations/sea_green.css","css/theme.css"]}

so it is no longer using custom.css

Oops. that last files_css is of course actually:

{"add":["css/animate.css","css/ajaxify.css","css/variations/sunset_orange.css","css/theme.css"]}

ok thank you very much for all those reports:

1. Options are a bit buggy right now: we're working on it, it will be fixed on next release. (it's a small issue with option.js we didn't noticed before)

2. To avoid the install/uninstall process, starting with next release, you'll can use in config.php: 'force_xmlsettings_for_survey_rendering' => true,
   If debug mode is on, it will force the rendering engine to get its values from the XML files rather than from DB.

Fix committed to master branch: http://bugs.limesurvey.org/plugin.php?page=Source/view&id=26507