As an organization, you probably need to create a custom theme to follow your organization design rules.
As a consequence, it would be great to be able to upload that theme on the WebAppBuilder of the ArcGIS Enterprise of the organization in order to allow users to create WebApps with that theme.
As custom widgets support has been added in ArcGIS Entreprise 10.5.1
(Web AppBuilder for ArcGIS now supports Custom Widgets in ArcGIS Enterprise 10.5.1 | ArcGIS Blog),
I think it makes sense to now support custom themes as well.
