Applying/creating a theme is not the issue - it works just fine, albeit being undocumented. The single configurator allows you to pass selections via the URLs which is great if you want to embed it into a portal or create dynamic links to redirect the user to Qlik Sense. But without retaining the custom theme with e.g. corporate colors, the single configurator does only half of its job, and 50% functionality is not enterprise ready.
Maybe I am underestimating the required effort, but to me it seems incorporating something in the likes of &theme=themename into the single configurator should not have taken more than 1 days of work.