Allowing unsigned code into the app bundle changes the app bundle and makes the signature invalid. That's how signatures work. The idea here is that a legitimately signed and installed app can then execute code outside the app bundle which will run without additional controls in place.
It depends. If you can add metadata to the bundle without it being detected (a problem that has cropped up with Linux repositories several times) then this is a genuine vuln. If OTOH it's something like "If you install a Python interpreter then you can use that to run arbitrary code that isn't validated by Gatekeeper" then it's a "Code execution results in code execution" issue. In the great tradition of journalists everywhere, the ThreatPost article never provided any links to any original material, so all we have is the writer's interpretation of what's actually going on,
Assuming the previous reply was by the guy who gave the talk, is it online anywhere?