I understand you want to use NLTK stopwords in GAE standard but I think you're confusing things a bit because one way or another you would need to have the file either in a folder or full in memory.
As you said, in GAE Flexible you could put RUN python -m nltk.downloader all -d /usr/local/nltk_data into the Dockerfile. In fact this command will download the NLTK stopwords file and place it into your container folder structure. In that sense it is totally equivalent to save the file yourself (as suggested in the thread you linked) or to make Docker save it for you, both end up with the file in a folder.
The alternative suggested by gaefan also implies to have the NLTK stopwords data stored although this time would be inlined in the application code rather than being in a separate file.
All in all, none of the approaches mentioned that far seems hacky to me and I would recommend any of them.
With that being said, if you really really don't want to have the file in your codebase you might as well store it in Google Cloud Storage and retrieve it. This way you may either retrieve it every time you want to do something with it or retrieve it just once and then store it in memory/tmp folder. However this option comes at the cost of application latency, ram usage and having to continuously check if the instance had downloaded it before.
