It seems worth mentioning here for future readers that the parameters from 3dvolreg could be applied with 3drotate instead (since 3dAllineate doesn't apply parameters the same way). Similarly, I would expect 3drotate would not handle the rotation parameters from 3dAllineate/3dWarpDrive appropriately. The matrix (matvec) inputs, on the other hand, should work similarly across the various AFNI programs that apply transformation matrices (3dWarp/3dAllineate/3drotate/Vecwarp/3dNwarpXYZ/3dNwarpApply/3dNwarpCat), although some require all 12 parameters on a single line.
