> In many cases this sort of change does
> improve clarity,

In some cases, perhaps. In the example you quote, yes, it does perhaps improve clarity. But here:

> -This function only handles buffers that are visiting files.
> +This function handles only buffers that are visiting files. 

there's no additional clarity. It could also be argued that, in those cases where the result is less natural-sounding it diminishes clarity, because it increases the cognitive load, even if slightly so.

> and it's a good habit to use the word "only" consistently

Ralph Waldo Emerson's dictum about foolish consistency being the hobgoblin of little minds has been quoted in this list often enough. If a change produces a less natural sentence, that should be taken into account over any "consistency".

> but then someone else who reads the sentence will
> internally vocalize it differently and misinterpret the scope of the
> "only".

We don't see a deluge of bug reports about misunderstanding the docs because of some (allegedly) misplaced "only".