A macro lens' maximum magnification can only be achieved at minimum focus. So to get maximum magnification you must move the camera towards or away from the subject to focus a specific area of it. That is the main advantage of using a focus rail.
In the case of stacking images, though, maximum magnification in every frame is probably of secondary consideration to maintaining a consistent field of view and perspective in each frame.
So the best practice would seem to be to use a frame rail to focus on the nearest part of the subject you want to be in focus with the lens set to the MFD, and then use the focus adjustment of the lens to take subsequent shots at longer focus distances. This assumes you are using a lens that does not exhibit focus breathingfocus breathing.