The planet was a key factor to the story and the power of deserts is what helped inspire the story but that doesn't mean the story was about deserts. Now I didn't read the entire 47 page interview so if there is some place there where he says it was about deserts please let me know. That would be a like saying Star Trek is about space ships because the ship is so important to the story. The story is about the people on the ship.

Ecology played a major role in the story but I wouldn't call it a theme because there is no ecological message in the story, on the other hand there are messages about politics, religion and power.

In a 1980 interview with Omni Herbert said

"Enormous problems arise when human mistakes are made on the grand scale available to a superhero... Heroes are painful, superheroes are a catastrophe. The mistakes of superheroes involve too many of us in disaster." [1]
Also:

"I had this theory that superheroes were disastrous for humans, that even if you postulated an infallible hero, the things this hero set in motion fell eventually into the hands of fallible mortals. What better way to destroy a civilization, society or a race than to set people into the wild oscillations which follow their turning over their critical judgment and decision-making faculties to a superhero?"

That is a theme