Another thing to consider is that if you use FLEX, the performance calculation assumes the Flex temp as OAT. E.g. if your FLEX is 65, then the performance is calculated as if it was really 65 deg outside. This greatly affects TAS (and hence GS) calculation.
If your actual temperature is less then flex (and it generally is), your actual TAS at V1 will be much less (like 10 knots) than the calculate. You will therefore need less runway to accelerate and decelerate in case of RTO.
As a result, your actual stop margin is significantly higher than the calculation (~1000ft in typical conditions). Bottom line - no need to worry about stop margin, even if the software shows 0