Android relies on specific "contexts" (SELinux). Auto tools automatically generate the fs_config files to ensure that when the ROM is reinstalled, a system app still has "system" permissions and not "user" permissions.
Kernel developers and those making small tweaks to the ramdisk. Step-by-Step: Using an Auto Tool to Modify a ROM auto tool unpack repack rom android
use a "Project System," where you create a dedicated folder for each ROM to keep original and modified files separated. Are you planning to modify a standard stock ROM Generic System Image (GSI) specifically? Android System Unpack-Repack Tool For Linux - GitHub Android relies on specific "contexts" (SELinux)