A focusing rail is still useful for macro work; it hasn’t been made obsolete by remote focus control.

Main advantages of a rail:

• At maximum macro magnification, many lenses only reach that magnification at minimum focus distance. To keep max magnification, you must move the camera toward/away from the subject rather than refocus the lens.
• A geared/micrometer rail gives very fine, linear, repeatable steps, which helps ensure complete depth coverage for a stack.
• Rails also help with tiny composition adjustments in macro setups.

Advantages of lens focusing:

• Often quicker and easier, especially if you only need a few specific focus points rather than continuous coverage through the scene.
• Remote/live-view control can be convenient for selecting overlapping areas that need to be sharp.

Tradeoffs for stacking:

• Refocusing the lens can change magnification/field of view due to focus breathing, which can complicate stacking.
• A rail can help keep perspective and framing more consistent, though one answer suggests a hybrid method: set the lens near minimum focus for the closest point, then adjust focus farther back with the lens if the lens has little or no focus breathing.

So: rails are best for precision, maximum magnification, and continuous stack coverage; lens focus is best for speed and convenience.