When to add the rye flour if it really makes a difference? I wish to use a small amount of rye in my wheat sourdough bread, because supposedly it improves the flavor of the bread.

What I'm wondering is whether it makes a difference if I introduce this rye flour into the levain or if it is better to put it into the final dough mix. What would make more sense from a scientific point of view?
Putting the rye in the levain will make a few positive differences: 


The rye will give the yeast a different food source, so the flavors the yeast produces may be subtly different
It gives the flavors from the rye grain longer to permeate the dough
Rye is often used in sourdough starters because of its natural yeasts. Natural yeasts add complex flavors, the earlier these are introduced the longer they have to contribute these flavors to the end result


These differences may be very subtle though, especially since you are adding a small amount of rye. There's no downside to adding it earlier, so no reason not to try.