Given the dearth of routes operated by AF that don't touch Paris/France at one end, I can only imagine that the text above is written from the viewpoint that customers transferring in Paris on wholly long-haul itineraries are considered to be "travelling outside the European Union".

However, what would happen in the case of irrops and your need to enter France is then difficult to say - your pet would most likely be quarantined until you returned to continue travel.

I have no experience whatsoever in travelling with pets.

I would advise you to pick up the phone and speak to an Air France agent.