To nitpick, I can only see "STARFLEET" stenciled on that door slab in the eels-to-ears scene - and the door slab doesn't appear to be part of the containers themselves, but a later addition by Khan.
Are there other instances of the word appearing on the containers?
I don't remember any, but can anyone tell if the stencil for "STARFLEET" is the same as "LOADING CAPACITY" visible on the actual interior of the bay's structure? It's minimal evidence, but could that be a connection? It might lend further Starfleet credence.
It's seems pretty obvious, even from that tiny image, that the "cargo carriers" were Starfleet. To go to the trouble of duplicating those Motion Picture
cargo pods to the degree they did, it seems their intention is apparent. It's especially apparent if they are at a different scale, which would require all new builds rather than reusing or retconning previous set/prop constructs. TWOK had tons of that. I didn't even think that workbee rig with the cargo clamps ever had anything but a filming miniature made of it. So unless something got built that never got filmed in TMP, that was an all new build attempting to mimic a previously visualized design element.