hi
the edit of the config is with commands (no files to be edited. maybe in good old 7 mode days)..
the global dedup is aggregate level. so as long as you set it only to the Volumes and AGGR that are flash based, you can use the like-to-like config as all-flash-fas system is coming pre-configured with.
look on the following TR from page 43 on the "Feature andConfiguration Interoperability" section and from page 44 on the "GeneralWorkload-BasedStorageEfficiency Guidelines" to find the best combination for your workloads.
https://www.netapp.com/us/media/tr-4476.pdf
Gidi