The setup generator only creates exe files. The MSI version can't currently be created by that tool. You can also use the MSI version for installation. After an installation, copy a logo.bmp file into the install dir. That image will then be used within the application.
Links to the setup can't be removed. Update search feature is also accessible by the user, also if updates are disables. Disabling updates means disabling the auto updater but updater can be executed manually.
The application checks, whether the user can install the update or not. If the user belogs to the administrator group, update is possible and if not, the update can't be installed. The update itself needs admin rights to be installed.