If you want to achieve true "extra quality" visual improvements in Citra, focus on the emulator's internal graphics settings rather than looking for modified system files. Once your keys are properly configured, try adjusting these settings for a premium experience:

This guide will explain how to obtain and use the aes_keys.txt file, ensuring "extra quality" (unlocked, high-compatibility) emulation by enabling the decryption of modern 3DS game titles. What Are Citra AES Keys?