Is it possible to use site_config.json to keep our custom key-value to be called by a custom script?
Or is it going to raise error (because there is key-value not native to frappe and erpnext)?
Well is very easy to test, but personally wouldn’t recommend using it, since the bench is writing to the file, and might modify it and delete your key.
The ideal way for custom key-value is to create a Single Type DocTypes
Single type Doctype