My employer recently introduced EFB's including the use of flysmart for performance calculations. A number of our Crew seem to have the same concerns as yourself. I think you need to remember that the accelerate stop distance part of the take off calculation ensures the maximum weight that allows to accelerate to v1 then stop ( I.e Margin being 0m ). So when compared to using paper charts for take off performance, we don't have access to stop margin information ( I always assumed it to be 0m anyway ), now we can see a figure some people are uncomfortable with it.
Personally I don't make any adjustment to the runway dimensions to increase the stop margin, but some people do.