In practical terms, flap setting DOES have a bearing on performance!
In the 747, the choice of using Flaps 10 or 20 for takeoff has to balance takeoff roll performance (better at Flaps 20) with climb performance (better at Flaps 10). While the 744 usually has plenty of excess thrust available, it is not the case with the 747 Classic. I have been in a situation where Flaps 20 was needed for runway limitations, but the airplane would not climb above 2000' until the flaps were retracted to 10. If you add windshear to that situation, it is clear that Flaps 20 would significantly detract from climb ability, possibly making recovery impossible.
The obvious answer is to not attempt takeoff when there is known low-level windshear. Also, do not attempt takeoff in marginal conditions when windshear is suspected or forecast. If you decide to risk it, optimize for climb performance, because that is where it will be most needed.