The JAA are looking to make sure you will not be incapacitated while flying and are fit to do the job. The airlines are looking for someone who can fly for 30 years so that they do not waste thier money training someone who will then be removed from flying due to medical reasons.
If you are obese, the chances are that you will have problems somewhere down the line in your career that will affect the airline, but the JAA may be happy that you are not about to conk out, hence the differing standards.