> So, if you make things harder and someone comes along that invests more effort to overcome, can you really call that a vulnerability?
Yes? This is defense in depth. Anything that bypasses a defense is still a vulnerability, even if your backup defenses protect you.
Defending physical hardware is indeed a theoretical impossibility as on paper, it will always be possible to make a perfect electrical clone of the original hardware and then modify it to suit. However, reality is different, and mitigations against physical access have become much more effective in recent years (iPhone anti-jailbreaking and the Xbox One come to mind as fairly successful).
So, this is a vulnerability indeed, just not a high severity one. One layer of the defenses are bypassed, but the remaining defenses remain.