I don't think you can property calibrate for it unless you also move the camera to compensate for focus breathing. I'm not sure if that would fully account for it either. That being said these things are only very noticeable pixel peeping.

Focus breathing can be compensated for. The "breathing" only changes the effective focal length, not the location of the camera, so you can map the pixels to match where they should be and bilinear/bicubic interpolate appropriately.

Shoot a checkerboard at both wavelengths each focused properly and then compute the mapping.

If you're shooting macro stuff then maybe you are changing the effective location of the camera slightly depending on the exact mechanics of the lens and whether the aperture slides with the focusing, but the couple of mm shift in camera location won't matter for landscapes.

Alternatively, use cine lenses which are engineered not to breathe, but they are typically more expensive for that reason.