Yes that is buggy indeed. But it is buggy already with the current API as you said, so when we provide an API to migrate existing users to, it's okay for this to remain buggy. 
That would only help if the external library also used that thread-local environment. Presumably this is not a Rust library, so a thread-local Rust shadow environment would be of no use.
Also even if this is a Rust command-calling library, I don't think the Rust standard library should have a thread-local environment just to work around the fact that the library-native approach of env passing in some crate is buggy. 
That's really a bug in that command-calling library and needs to be fixed there. There is very little the people calling the command-calling library can do about this, they need to get their dependency fixed or use another one.