"applications from people who are nominated by a State/Territory government whose nominated occupation is not listed on the CSL." will be processed behind CSL.
No, the FAQ says the new directions apply to "all applications in the pipeline that have not been finalised". Seems pre-grant does not mean finalisation.
Q9 What will happen to those applications which are in the final stages of processing and where the Department has requested applicants to provide health and character clearances?
The new arrangements apply to all visa applications, including those in the final stages of processing. Applications in lower priority groups cannot be processed further until those in higher priority groups are finalised in accordance with the priority processing Direction.