Metroid Prime’s Chozo Lore entries — wall inscriptions found throughout Tallon IV — are presented in an English translation by the game. What Retro Studios also built into the disc: the Chozo script visible on the walls of Phendrana Drifts and Magmoor Caverns is a functioning cipher.
Players who photographed the inscriptions and mapped them against the in-game Chozo alphabet — which appears in the Artifact Temple and can be decoded from that single reference — discovered that the wall text in the Ruins says something different from the English translation displayed in the scan visor.
The wall text versions are shorter and more archaic in phrasing. Several contain passages that do not appear in any scan visor entry and describe the Chozo’s relationship with the Leviathan impact in terms more emotionally explicit than the formal lore entries.
Retro Studios built a second layer of Chozo Lore — one accessible only to players who decoded the cipher from the Artifact Temple and translated the wall text manually. No official source has ever acknowledged this layer or published its full contents.

Currently on my first run and now I have to go back and look for this. Worth the detour.
Found this by accident on my third run. Came here to understand what I was actually looking at. Great write-up.