Since that post, we've seen many more instances of the Squidhenge glyphs disappearing. They tend to "glitch out" (disappear) during Theater Mode replays, for instance- independently of how they appeared in-game at the time. This alone leads me to believe this is a graphics glitch and not a mysterious Easter Egg clue. Of course that's just my opinion. For me, the appearance of the Sad SuperMono glyph on Squidhenge is clue enough.
Something for anyone interested to try:
Go to squidhenge.
Mess around for a while.
Go through door D06-008 (see
map) to access the adjacent building interiors.
Mess around for a while.
Return to Squidhenge.
Mess around for a while.
Exit the game and view it in Theater Mode.
In Theater Mode, switch to Floating Camera Mode by hitting the Y button.
Observe Squidhenge as you mess around and then leave to enter the buildings.
Check to see if the glyphs change at all. IIRC, this sort of action was what led me to see the glyphs glitch out and then even reappear.