If using AAdvantage miles is one reason. I've found that booking through JL does not always bring up as many routing choices when departing from some smaller US cities.

Also cost can vary widely depending on whether booked through AA or OW partners, and can go in either direction. An upcoming trip has me flying Reno-Almaty then Istanbul-Reno. The outbound was around $2k cheaper booking through AA (on QR metal for the longest legs), while the return was several hundred less to book through QR. Interestingly, an open jaw route booked through either carrier was pulling far fewer routes and way more expensive.