I take it the margin you refer to is that resulting from GS being lower and thrust being higher at the actual OAT when using a flex takeoff temp.
If so, the margin is 'extra'. The figures should come out (almost) the same if you put your flex temp back in as your OAT and look at the TOGA figures. I say 'almost' since it is an iterative process and small differences/discrepancies can creep in.
Ultimately you do have a bit of performance margin on the safe side, abive the FOVE figures.