Thanks for checking in, I don't really get why this needs rewording but I don't mind the tiny change either.

The first motivation is consistency: If I had read, for instance,

  -o, --out-dir DIRECTORY  Set explicit output directory.
  --config FILE            Set explicit configuration file.

I probably wouldn't have noticed anything (say, the area for improvement). Because it would have looked consistent. But seeing

  -o, --out-dir DIRECTORY  Set explicit output directory.
  --config FILE            Set explicitly configuration file.

made me wonder why "Set explicit [noun]" and then "Set explicitly [noun]?"

Second, my understanding of the semantics is that the options let you "do something explicitly" (which, btw, sounds more natural than "do explicitly something") and not so much "do an explicit thing").

Ah, that makes sense. Thanks for explaining. :)