How to store system app's settings on /system partition?
You can't. Configurations / settings / cache / databases of every app (system or user) are stored on /data or in /sdcard/Android/ for some apps. That's why /system partition is of limited size as compared to /data. Android works that way. Apps aren't built to read and write settings to /system partition as it holds a read-only filesystem, only changed during OTA updates. A read-write /system partition won't fit into Verified Boot  mechanism implemented by Android for security and to prevent malware attacks.

Further reading: Android Partitions and Filesystems