Talking with our CAA FOI about this last week he claimed that it was to deal with helicopters and smaller business aircraft (a couple of our engineers own an FAA reg PA28) which are registered outside the EU, cannot transit back to their countries of registration and in some cases have been found carrying out illegal public transport across the EU, occasionally with dodgy maintenance backgrounds.
Typically for the EU they have used a sledge hammer approach because they have limited oversight of these aircraft and haven't taken into account the EU PPL holder who has an N reg machine for his convenience and has no intent to use it for anything but his own business/pleasure.
Basically EU Ops paranoia strikes again, MAKES ME