The way I figure income is take after-tax income, and add back 401k and 457 contributions. This is the amount of income we have under our control - we either spend each dollar or save it (401k, 457, roth IRA, additional mortgage payments, taxable account).
The other factor that I personally ignore is my wife's defined-contribution plan at work - I ignore this from savings rate calculations because we don't control it - she has a mandatory 3% contribution with a 3.21% match - we can't change either of these numbers. I suppose our savings rate figure is about 1% lower than it would be accounting for this, but I like to err on the side of caution there. Added bonus is that there is just a little bit more upward pressure on the 'stache than we are planning on - makes it more likely that we'll hit the projections. If you do want to account for this, be sure to add the deferral AND the match to both numerator and denominator, lest things look a bit more rosy than they actually are.
I think figuring the savings rate on pre-tax income is unnecessarily discouraging. Once retired, you'll have much more control over your taxable income - post FIRE tax rate can be 0%, or at least very low.