I am working on deploying a ClickOnce Application build on .NET 4.5 Here are the facts:
It's not that complex.
1st, you need to just sign the manifest using your cert.
2nd, you need to install that cert to "Trusted Root Certification Authorities" store on your client PC, this you can do by checking your cert detail and then install following the wizard, ensure you choose the right store.
This step will change the unknown publisher to the name in your cert.(As the publisher is now in your trusted root CA, so it's no longer "unknown") but you will still have the prompt to asking for installation confirmation.
3rd, you can again install the cert to "Trusted Publisher" store on your client PC, then the publisher is trusted publisher, you will no longer get prompt, the installation will just happen.
Hope this will help someone still facing the issue.