In this example the title and subtitle will be configurable, but not the logo. There is only one link and both the label and url can be set. Only the Directions widget can be switched on and off. The others, chosen from a wider list, will always be included in applications created from this template.
The released version of Webb AppBuilder is now available in ArcGIS Online. Note: the article was written during the beta release so there may be some small differences.