If my point of focus is bang on an AF point (with my canon 60mm Macro lens) I will leave it in AF, then tweak with manual focus. Usually however it does not work out like that.
In AF, that leaves focus and re-compose. However with Macro the DoF is so shallow any movement in the camera between focus and shutter action will take the subject out of focus. The answer is MF.
Another issue (albeit a bit more technical) is that focus changes lens extension (whether internal or external) which changes magnification. This can be crucial in some shots, so fix your extension (=magnification) and focus by moving the camera forwards or back.
Unless you have a lens with focus limits, then many macro lenses will hunt which can be a real pain if you have only a moment to catch that fly.....