Interesting you should post this because my project this weekend is to deduce as much from our various income sources. I have found this to be as complicated as I expected because neither my tax documents nor my tax return actually has the denominator laid out for me in full, because of the subtle differences between gross earnings, deferred income, wages, etc.
In the example you cite, the 401k contributions are included in the total take home pay as part of the gross pay, so it is part of the take home pay. As you say, you could have taken it home (less taxes), but in my view because it is now in an account that you have control over, similar to an HSA, it is part of your denominator of money you have brought home.