I believe the confusion here comes from the ambiguity of the "It's a shame" comment, as it could be "It's a shame [that the gem cannot be safely stored in its home country due to the political situation]" or "It's a shame [that the gem is not stored in its home country despite the political situation]".

The "despite all evidence to the contrary" remark was in response to interpretation B when it seems interpretation A was the intended meaning.