The Mars Longship, DARC-1, Super Big Bertha, Majestic, soon to be released Super Mars Snooper, the RTF Saturn V, the RTF Artemis/SLS…there’s a few E2X kits aimed at the general sales/box store market that come boxed - like the Astro Cam set and stand-alone rocket, the Mars Hopper and Space Force Centurion as well.
In addition to those already listed, the Ghost Chaser is boxed. Also the RTF Athena and the ARF Phantom Blue have always been and are still boxed. The other still-available ARFs (Chiller, Spirit) are also boxed.