I have owned a few 980SSB radios since they were first introduced, including the earlier boards and later redesigned boards. They all have dual clarifier controls, as have the radios that friends have owned.
I had noticed the difference in the stock cover photo several years ago and I believe it is simply an early design/prototype photo (probably the very unit that was sent to the FCC for testing), but the dual clarifier was added to the final production unit. The disclaimer on the box about the photo possibly being different would seem to support my theory.
There are two different boards that are found in the 980. I believe they redesigned the board around 2016, and that gave you the “beep-delete” option from the front panel (there are other significant changes internally). The original board has an SWR bridge circuit board mounted to the rear wall of the chassis. There is a screw on the rear panel to the left and below the antenna jack, that holds the SWR bridge in place. If your radio has no screw in that hole, you have the newer board, because the SWR bridge was redesigned and incorporated onto the main PCB.
But to my knowledge, all production 980s had dual clarifiers.