You are correct on
When your application requires CLI commands (such as some CRON-related cleanups) the .htaccess file is unavailable, so the variables will not be correct
You can run those cli commands if your are not on a shared hosting environment. In the post i have stated that .htaccess is for those with a shared hosting plan (like the godaddy ones).
You wouldn't use .htaccess if you owned the server where the app is deployed. You would go with the second option i have provided. Set the evironnment variables on the system level. That way if your application requires CLI commands the variables would still be correct.
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