Hmh? The ribbing, the curvature and the way they sit on the ground comes straight from ST:TMP - while the Botany Bay
containers (or fuel tanks?) were angular but smooth things of seemingly much, much
greater size. That is, if Khan's original sleeping stations were inside one of those containers, they'd be at least four times the size of the ones he lived in on Ceti Alpha V. And if Khan's sleeping stations were inside the pencil-like hull of the ship instead, then the containers would be absolutely huge in comparison.
Botany Bay must have had some sort of supplies onboard. Even Khan would need materials to build a home on a new planet.
Assuming he ever wanted such a thing.
For all we know, he just wanted to get away from Earth for a period of time, then effect a triumphant return. His plan all along might have been to sleep in a ship that would send a signal assured to lure in fellow Earth vessels, hopefully after Earth had forgotten about Khan... Or then simply to loop back, and the signal was an error that caused Kirk to locate Khan and force him to switch to Plan B.
The rest of the ship was probably towed to a Starfleet facility and the historians went over it with a fine toothed comb.
Doesn't jibe well with the idea that Kirk kept Khan's existence secret from basically everybody, or at least from his Starfleet employers.