I don't think you are familiar with real movie sets à la Kubrick or the recent sets built by Mel Gibson.
For Full Metal Jacket Kubrick had real buildings torn down, instead of using already destroyed ones or ridiculous cardboard sets. You might want to google the other crazy sets and props Kubrick had built.
For Apocalypto Gibson had built a Mayan city from scratch. Even the paint for the buildings was made by hand, as it would've been made back then.
The "movie sets" you are referring to are not art. They are commercial garbage. No harm lies in replacing those with CGI.
Whether I'm familiar with the examples cited (Kubrick and Gibson) or not (and I am), you are citing outliers; exceptions, not the rule. Personally, when making a broad statement, I'd ignore such examples in favor of what's typical.
Can movie sets be great art, and can CGI be crap? Of course. And as you admit, there are movie sets that are crap, and CGI that is great art. So why hang onto the notion that there's a "real" and "fake," legitimate or illegitimate, in a business that is entirely built of illusion?
It's all about the willing suspension of disbelief. Poor-quality work may be a distraction that can break the illusion, or prevent it entirely - and that's true whether we're talking about scenery or the actors that chew it.
Art. Artifice. Artificial. If you want real, you go sit on a mountaintop and experience the reality of it - the breeze, the sounds, the aching muscles and drying sweat, textures, scents, sunlight and shadows, temperature, flora, fauna, stone and sky.... You want art? You sit in a chair and absorb Ansel Adams' or Claude Monet's or Aaron Copeland's, or John Muir's, Akira Kurosawa's, Auguste Rodin's, Hayao Miyazaki's, Martha Graham's, William Shakespeare's, Louis Comfort Tiffany's, Robert Frost's, Frank Lloyd Wright's...
impressions of nature.
You are putting the medium before the message. All we ask of art is that it speaks to us, that it moves us, that it inspires, terrifies, enraptures, enrages, comforts, transports... the artist is a person who can conceive of a way to do that and who has the mastery to deliver what he/she imagined; so that their work can capture the hearts and minds of those who experience it.