How many machines are you distributing to? The package as it is downloaded from App Builder is actually installable on any machine you like, provided you're willing to acquire a developer license on that machine (which the install script will do for you) and trust the self-sign certificate (which the install script also does for you). If you're only deploying to a small number of internal machines that's likely your best bet.
If you're talking about an enterprise-wide deployment to many, many, machines, then you'll need to re-sign the .appxbundle and .appx files with a certificate your enterprise machines already trust. This can be any app signing certificate, but must be trusted by your enterprise machines. If you get to the stage where that's something you want to do I can provide some information on the command lines to do that.