Flying low does not mean "scraping trees" but for example Glass G airspace (uncontrolled basically) is everything under 1200' not near airports etc. For a lighter than air craft 1000 feet off the ground is quite a big margin of error actually.

And I doubt one would be flying something like this in bad weather anyway. One would just wait for the next weather window.

And one could easily take the ship into 4000' or something like that and still have minimal amount of other aircraft around once outside of airports (proper commercial jets fly at 40k feet or so).