createWindowsInstaller allows to specify a file that will be used instead of the default loading spinner. This option is not used in WinPackager.packageInDistributableFormat.

I suggest to add loadingGif: this.metadata.loadingGif to the options in function packageInDistributableFormat and add the path to the development package.json like
{ "build": {"loadingGif": "./build/install-spinner.gif"} }