A lot would depend on whether you need continuous focus through the scene or have more discrete points of interest. A micrometer (geared) rail can make it very fast and easy to make sure that you have complete coverage of the depth of a scene with greater precision than manual focus simply because the adjusting mechanism is finer and the scale is linear. Like creating a good HDR sequence, not missing an exposure along the way makes the software's job a lot easier. Live view and AF can be quicker and easier if you have, say, overlapping elements that need to be sharp but large (relatively speaking) gaps in the image field where nothing in particular needs to be captured, but it can be difficult to pick appropriate points of focus if you need continuous depth.
That said, if your lens is a true internal focus lens, the field of view will remain constant as the focus changes. If you use lens focus with such a lens, the relative positions of everything in the frame will be consistent from exposure to exposure, and you will get more accurate alignment/stitching, less distortion to deal with and less detail loss (no interpolation or scaling will need to happen). The macro rail, or a unit-focus or hybrid-focus lens will always change both the magnification and the relative position of things in the image, making the construction of the final image more destructive. It would then be worth using the lens focus (manual or AF) even if it's slightly more difficult to do so if ultimate image quality and resolution is the goal (and let's face it, our cameras are often capable of giving us much more than we actually need, so throwing away a few pixels isn't necessarily an unforgivable sin). You would need to test your lens to see whether or not it actually keeps things in place and in perspective as you focus.