IME the nic will subtly (or not so subtly) affect the final flavor, so for me it's always in the mix. And it WILL affect TH.
That, and because I mix a large batch of unflavored at just below my preferred PG and just above my preferred nic level. Flavorings are generally in PG, so that brings the ratio closer to my preference, and their addition also brings the nic down a little. Like DaveP says, makes mixing small batches a snap. Measure flavors, top up with the premix. Done.
If you mix a wonderful flavor without nic and add the nic, and it changes it, you're back to square one.