If they are using visual studio to develop the program, they have to sign with visual studio
When you are developing with VisualStudio manifest files are created that need to be signed. In order to sign them correctly you'll need to use VisualStudio in order to sign them correctly. I have attached a walk-through that will help you set up and sign your manifest and click once programs.
digicert-ClickOnceVisualStudio2013Walkthrough-060516-1409-34.pdf