Using Easy Code Signing With Wix Bootstrapper
You can use Easy Code Signing to sign a bootstrapper exe. You might be running into your setup refusing to install because of a 8007000 error. This is because the Wix bootstrapper has a file inside its bootstrapper exe that are not signed. You need to extract the file and sign it.
You do this with these commands after you build your bootstrapper.
insignia -ib "[pathtoyourinstaller.exe]" -o engine.exe
ecs "/p:[pathtoyourinstaller.exe]"
insignia -ab engine.exe "[pathtoyourinstaller.exe]" -o "[pathtoyourinstaller.exe]"
ecs "/p:[pathtoyourinstaller.exe]"