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WP-CLI is the best way to perform long-running processes in WordPress, always!
If you don’t know about WP-CLI, I suggest watching some YouTube tutorials, or some documentation about it. You shouldn’t use it only for Media File Renamer, it can be used for various other tasks.
Then, there is nothing specific about WP-CLI in regards to Media File Renamer 🙂 You don’t need to be in a specific directory, WP-CLI runs in the context of your website (so it’s not related to the directory you are in).
For your 3rd question, it’s for renaming a specific Media ID.
I hope it helps 🙂