This pilot suggests the possibility of flaps being accidentally retracted instead of the landing gear.
Explains why the landing gear was never retracted and the aircraft seemed to wallow.
[..]
But it doesn't explain the possible deployment of the RAT which is audible in one of the clips (but as of yet unconfirmed).
I don't put so much weight on the landing gear still being down on these altitudes. On the video the jet clearly developed problems at or closely after V1 speeds. Raising the gear will improve drag, but if you need to bet on putting it down somewhere on the ground fast, then having the gear out can take a major part of the beating. Unfortunately, they didn't really have the luxury of some field to land.
Sadly, a similar confusing thing could be done for flaps too. The captain on British Airways Flight 38 made this intervention to glide a bit further to atleast crashland on the airfield perimeter. They could have changed it by accident after rotation, or thinking it would glide them just slightly further.
What I don't really fully understand from that video is the power on stall explanation. Typically stall recoveries start by pushing the nose down to gain speed and decrease the required AoA to fly safely. If this jet was still producing thrust from its engines, it would have been a very sticky thing to do so close to the ground.
Unfortunately, these big jets can be quite tricky to climb safely (in contrast to A320s/737s which climb like rockets). These jets can require high speed climbs when they are heavy and need to keep a higher speed for a safe climb profile. I'm not familiar with the 787 if it requires this, and subsequently what its rotation and initial acceleration speeds/altitudes are.