Didn't have time to look at the video first time through .. boy, but that's an old training video .. I can recall it being introduced, guessing now, around the early 80s ? As I recall, Boeing led an Industry study group on rejects and the video was one of the outcomes. Nonetheless, it's pretty good gen. Memory is a bit ragged on this .. if the video is the one referred to in the link at the bottom of this post, it will have been developed somewhat later. However, I seem to recall having seen it during recurrent training sessions in the 80s at AN - perhaps that might have been later in NZ - doesn't really matter.
Ref the three seconds .. all OK, the long-established one second time sequence to reconfigure expeditiously for the reject (which had been the basis for most certifications for many years prior to A/L 42 - watch guys in the sim and be startled at how many take somewhat longer to achieve the reconfiguration to throttles closed, boards up, and max braking .. and that's with them primed for action .. ) plus the A/L 42 two second pad at V1 to provide a bit of a pad for things such as crew startle response and so forth ie acknowledgement that one second really didn't cut the mustard. If my recollections are correct, the original 707 certification program introduced the one second timing ?
I would hesitate to call it a margin. At best it's a bit of fat to acknowledge that the typical reject crew is going to be hard pressed to get the thing stopping in under three seconds ...
Main thing for all to keep in mind, that time pad disappears VERY rapidly and a tardy PF can find him/herself eating up stopping distance with considerable ease before the reconfiguration is completed ...
Another useful reference is
https://flightsafety.org/files/RERR/...gSafetyAid.pdf