I've found that during IRROPS, you can deal directly with the airline when tickets are purchased through a 3rd party site. However if you miss a flight or need to make changes, you might need to call Expedia and deal with them instead of directly with DL. Expedia will charge a change fee and DL will charge another change fee.
Overall I think it relatively safe to book airfare through these third party sites. But the fact that the fare is so much lower throws up red flags. Read the fare rules very carefully to understand your risks and rights.