What a good question! At Future.Travel we have issued thousands of tickets. The price of each one is different.
In practice you can be sure that the LCC or discount airline ticket is costing the agent more to issue than a full service airline. The full service airlines subsidise or even pay a rebate for issuing their tickets via GDS or direct airline agents connection. The LCC’s normally charge per passenger, and per segment flown , so the ‘price to issue’ a ticket may be very low as in a full service GDS airline, or more expensive on a very linear expense scale for an agency who does a group booking on an LCC.