If you read the documentation, it states folders in green "Folders for custom files, part of the export package. You may need to create these folders manually." So if you have a folder in the
/App_Themes directory named the same as your site's code name it will automatically be exported. So while yes, App_Themes were initially meant for different themes on your website in a standard asp.net website, within Kentico, by default if you use the OOTB CSS Stylesheets and your stylesheet's theme tab, it will give you access to all those files within the UI. Whereas if you simply place them in the root of the file system, you'll have no access to them through Kentico at all.
Really the only images and files we put in the
/App_Themes directory are font files and any hard design related files, those files we don't want a content editor to be able to access. Otherwise we place all other resources in the media library and
/CMSScripts/Custom. Since you can specify where those resources from Gulp and other third party add-ons can go, I'd suggest using the respective places as shown in the export documentation.