I was running into the same issue and just found out what I was doing wrong. It looks like you're doing the same thing.
The explanation both the documentation and @coreyward give are correct, however, note that while corey implies they're two different approaches and the issue might be that they're conflicting, they're not, they do different things - so that code of yours is fine.
What's wrong, though, is that you're console logging process.env. And as it turns out, this will always output an empty object even though the variables might be there.
You have to console.log(process.env.GATSBY_APP)
directly to see any value.
(Reference)
This is essentially an extension of what Corey pointed out in his "finally as a side-effect" section, however, the way he's written it implies it's an issue with destructuring - but it's not limited to that.
In my case, I was doing the above error AND not exposing the variables with GATSBY_ properly, then while testing I started logging the whole env object like you while I searched for the cause. This meant that even after I added the correct GATSBY_ prefix I still couldn't see anything.
So in short, it's probably only your console.log line that's an issue - access the variable directly, not the env object as a whole.