A cargo shift typically manifests itself with the nose coming up to an unusual attitude and the crew being unable to control it. In an airliner, where the cargo is stored in containers in the belly, I’ve never heard of a cargo shift.
Each one of those containers gets locked into the floor, so even if one came loose, the position of the others would block it or, that one container by itself wouldn’t be enough to cause a fatal center of gravity shift.
My understanding on the 787 is that the gear handle is on the panel, not the throttle quadrant. They’re quite different in location, shape and feel precisely to prevent this kind of mistake. The gear handle is shaped like a wheel, and the flat panel is shaped like a flap. This was a change made in the 1940s because pilots would confuse similar switches.
The 787 has takeoff warnings for the following:
CONFIG DOORS
Cargo and/or passenger doors are not secured and locked and either engine’s thrust is in the takeoff range on the
ground.
CONFIG FLAPS
Leading edge and/or trailing edge flaps are not in takeoff position and either engine’s thrust is in the takeoff range on
the ground.
CONFIG PARKING BRAKE
Parking brake is set and either engine's thrust is in the takeoff range on the ground.
CONFIG RUDDER Rudder trim not centered when either engine’s thrust is in the takeoff range on the ground.
CONFIG SPOILERS Speed brake lever is not DOWN when either engine’s
thrust is in the takeoff range on the ground.
CONFIG STABILIZER
Stabilizer not within the greenband when either engine’s thrust is in the takeoff range on the ground.
There are more takeoff warnings in the 787 than any airplane have flown.
I don’t doubt the ability of a crew to miss warnings, however, because it has happened before. Here is one of many examples where a crew continued to takeoff despite the warning horns blaring the entire time. It did not go well.
https://en.wikipedia.org/wiki/LAPA_Flight_3142#
I doubt the airplane was severely overgross, however, there have been several instances where the crew inadvertently entered the wrong data in the flight management computer, and took off with the wrong reference speeds. Again, there are many instances, here’s the first hit I got on Google.
https://skybrary.aero/sites/default/files/bookshelf/33358.pdf