Hello Godot,
I guess the main reason why 3drotate and 3dvolreg cannot be used one after another is mainly because each step involve in some sort of interpolation. Doing the interpolation more than once can easily destroy the data badly. By default, both 3drotate and 3dvolreg use -Fourier as the interpolation method.
However, I heard that interpolating the data twice is not impossible using sinc inpterpolation method. But then neither 3drotate nor 3dvolreg have sinc interpolation as an option to choose from.
Thanks for your previous comment.
Ricky