i think their fares are cheaper because they want to compete with the local and other airlines.
regarding the ticket being cheaper from dubai via doha, i am sure one has to purchase it from dubai and the travel must commence from there too. i am sure there must be a catch!
even though direct flight are cheaper my emirates ticket to karachi(doha dubai karachi dubai doha) is more expensive than the direct flight from doha to karachi!!! the problem is i need to visit my parents in dubai and am forced to travel with emirates.