Should (or once) the EU gets its operational military HQ, the 'Berlin arrangement' (whereby DSACEUR uses NATO structures as part of an EU-led operation) becomes a little overtaken.
NATO-EU cooperation is moving forward under other frameworks.
If true though (the story in Times put up by the OP), then the saying 'one can rely on ones enemies; it's friends that need watching' springs to mind.
Batco