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Of course there is a difference in how to do focus stacking! With elder lenses you need to move the camera with lens. With AF lenses you use Helicon remote and after doing the stack shots, you put them into Helicon focus to layer them.

 

With Non-AF lenses one is forced to buy additional hardware - that makes the advantage of "cheap" vintage lens pretty much eaten up.

 

More than that: With manual macro lens you also need an extra power supply for the stepper, for the remote control it comes to being equal because Helicon isn't part of a camera - but they could make an app for Sony and their in-camera-apps. The Sony menus and firmware already are so huge, so it would not matter to put in another 100MB or so 

Moving the camera with the lens will not work well (changing POV for every shot). Refocussing the lens happens the same as with AF lenses, by hand in live view. If you want to use Helicon Remote, that is fine, and yes, then only with AF lenses. Issue with refocussing the lens is the changing FOV.

The best way to go is leave the POV the same (not move the camera), leave the lens geometry alone (no focussing the lens between shots) but move the lens itself (so, use an old macro lens which moves all elements, or use bellows).

 

In case of the 55mm f3.5 that means no extra hardware or software to purchase, then.