how to specify the file directory in drush config:status
There's no option to do this with drush config:status. See the drush 10 documentation for config:status.
Presumably, you want to check if the config has changed so you can export it to your sync directories. Why not export it to them directly? If there are no changes, there will be no changes. But if there are changes, you'll see them in your repository, e.g. with git status.
I've always used Moshe's recommendation from comment #7 in your linked issue:

You must get your configuration right before you run a config import. Specifically, the config in the import must represent the values AFTER hook_updated_n runs. The developer workflow I advocate is to run the hook_update_n() locally, run drush config:export, and and then commit the results. Only then is the saved config ready to be imported.

I.e., start with a site in a clean state in your local environment:

Update your project(s) with composer.
Run drush updb to perform the db updates
Run drush cex to export any config changes made during those updates
Add any changes to your repo, commit, and push.
Pull the changes on your new environment
Run drush deploy