I'd like to share my technique of doing some modest customizations to the Qlik Sense Server Hub which involve editing the source code:
Changing the favicon
Changing the accent color of the header in the hub
Changing the image at the upper left hand side of the hub
1. Changing the favicon
First, you'll need to make a .ico image which is 16x16 pixels named "favicon". Use a site like https://www.icoconverter.com/ to convert from other image formats. Navigate to the folder located at ~\Program Files\Qlik\Sense\Client and replace the icon named "favicon.ico" with the one you have created.
2. Changing the accent color of the header in the hub
Qlik Sense Server Hub Header
Navigate to the file located at ~\Program Files\Qlik\Sense\Client\hub\hub.css (a minified css file). Find the css class "hub-toolbar-footer" and change the background attribute to the color of your choice. To edit this file, I use the program Notepad++ which you must be able to run as an administrator.
3. Changing the image at the upper left hand side of the hub
Create a .png image which is 346x66 pixels and name the image "sense-server". Navigate to the folder located at ~\Program Files\Qlik\Sense\Client\hub\img\core\logo and replace the image named "sense-server.png" with the one you have created.
Things to keep in mind; when editing the code, always keep a backup copy of the unedited files or pictures in case something goes wrong. You will need administrative access to the files mentioned above. To see the changes take effect, you must clear your browser cache. These changes will be removed when you upgrade versions of Qlik Sense. You will have to reimplement these changes after you upgrade, so keep track of your images. These changes have been tested on Qlik Sense Server November 2018 (12.44.1) and are not available on Qlik Sense Desktop.