Select TOGA, or calculate the performance from an intersection whilst taking off full length, reduce runway length, enter a tail wind...there are many many ways to increase your margins. But why bother? You know what performance is based on and use that knowledge. Otherwhise stay in bed.
Or use TOGA+flap3 all the time!
The only time I seriously consider lowering the Flex and the speeds is in LVP's, for very obvious reasons.
In more than a decade using the software I have only seen one absolutely limiting takeoff, i.e. TOGA, F3 and close to zero margin.