I treat them differently in two ways. 1) I apply tax drag factor to after tax accounts that I don't include in retirement account returns. 2) My current plan calls for Roth ladder conversions over about 20 years, and I apply a 20% effective tax rate to each annual conversion. So if $100K comes out of my traditional and over to Roth, $20K comes out of my after tax accounts to pay the tax man.
ETA tax drag.