E.g. I had a really weird bug in a script, git seemed to break for no reason, until i figured out that some other script had exported GIT_DIR which pointed to the git top level directory. The name of the variable isn't bad if want to save that directory. But git uses GIT_DIR as the location of the .git directory it should look at when it is defined.
Using environment variables is kind of like using global state, it can often cause weird behavior at a distance without a clear path of influence if you don't know exactly which environment variables are used by all your scripts.
I write a lot of tools in Haskell, where 'getEnv' is an "IO action" whose type prevents us using it inside most code. The simplest way to handle this ends up with a "functional core, imperative shell" model, e.g. most of my CLIs have the form (where 'interact' takes a pure String -> String function and uses it to transform stdio):
main = do
foo <- either error id . parseFoo <$> getEnv "FOO"
interact (doTheThing foo)
doTheThing :: Foo -> String -> String
doTheThing = ...
This is also trivial to test. Some languages make it easy to replace env vars inside a single expression (e.g. bash), but others require us to set and reset the global environment, which is painful and error prone (especially if tests are run concurrently).It's not universal though; you can't in C or shell scripts for example (although, if you really want to, it's not hard to assign a global). I never had the need to inspect commandline arguments beyond the main() function though.