I have seen a number of colleagues of mine start getting jittery with such a low stop margin. To add to the points already discussed here, there are a couple of other safety factors inherently built into the EFB computation.
1. EFB assumes 50% of the headwind and 150% of the tailwind for take off performance computation.
2. EFB assumes Reversers to be inoperative for dry runways..
Factoring in these conservative assumptions the actual stop distance would be less than the one indicated in the EFB so the stop margin would be a lot more than the calculated figure