I should add there is a perfectly valid reason why Allen used the word 'guarantee' there and it is connected with whether the EU would have accepted Scotland as a member if they had voted for independence. That could not be 'guaranteed', which is why it was perfectly reasonable for Allen to say it the way he did.

Yes, if his understanding of what he said is the same as your reading of it.
But if that was his intended meaning then it makes no sense of the immediately following query "How does that equate with what has happened since?".
That query seems to suggest that he understood it as a guarantee that Scotland would remain in the EU no matter what UK subsequently did.