I think we have to remember that the magic sky moments are very atypical. Even being lucky enough to capture one is much a matter of luck (even with research, constant following the weather reports, etc.). The romantic (I believe it would be the romantics) took advantage of light and clouds, etc., in their paintings. But it's a matter of trying to create an effect, a feeling and and not necessarily a documentary record of the place. I think it becomes a problem only if it's passed off as a documentary.
If you compare the skys in these, you can see the results of added work:
http://www.pbase.com/image/24185218
http://www.pbase.com/image/24185245
For that matter, checking the rest of the gallery shows the changing skies of the day.