Update from /e/OS 10

Regarding your list of locations, from my understanding, /data/app/ should contain all user installed app apks (including apps installed to work profile), /data/data/ contains the apps data from default profile (user 0), /system/app/ contains the system apps apks.

/data/data/ is interchangeable with /data/user/0/. Though, there is additional app data stored here: /data/user_de/0/ (mostly cache, and preferences). If you use a work profile (or Shelter/Island/Insular) you should also backup work profile related data: /data/user/10/ and /data/user_de/10/.

Does /media/ contain your internal storage data? In my case of a FP4 internal storage is located at /data/media/, but maybe that path differs from device to device. Internal storage of default profile (user 0) is located at /data/media/0/ (/storage/emulated/0/). Internal storage of work profile is located at /data/media/10/ (/storage/emulated/10/).
For better understanding I found this article on Android data storage paths which kind of reflects the current state of 2023: https://android.stackexchange.com/a/218507

From what I know, backing up the locations mentioned above should provide you with a complete backup in terms of all individual data on your phone (but not a bit-perfect or full block-level backup, which is not needed IMHO, anyway).

If you are looking for a file-system level backup method, I recently proposed a new backup solution which is completely independent from adb: [HOWTO] End-to-end Encrypted Full Backup and Restore Solution for /e/OS using Termux and restic