We actually recommend using the non-residual data for smoothness estimation of rest data for this reason, and afni_proc.py examples generally show getting both estimates (even just for education). But fortunately, the estimates tend to be pretty similar, so it isn't usually the end of the world to use the wrong one (occasionally, it does end the world).
The smoothness of the regression inputs tends to be just a touch higher than that of the residuals, for whatever it is worth.
- rick