Again, with respect to flag burning, one should not confuse supporting the rights of one's non-violent self expression, with approving of the expression itself.

"I disapprove of what you say, but I will defend to the death your right to say it." Attributed to Voltaire in S.G. Tallentyre, The Friends of Voltaire (1907), p.199.

In the case of flying two flags, one over the other, this is a breach of etiquette and, intentional or otherwise, is disrespectful to one at least one, if not both nations.