There're three endings: one where you don't 100% the game (tablets + bestiary) or do the shields & serpents puzzle (the "bad" ending), one where you either 100% the game or do that puzzle (one of the two items, the "normal" ending) and one for completing everything (the "good" ending). If you got the last one, that's the best ending! Congrats! Though, now I may have to add a super secret ending in...
And, in regards to your question, it was retroactive, though I wish I'd had the foresight to add something like that in at the time. Though, I hadn't even made Transmute (Polymute's other prequel game) at that point, so I had no idea things would connect as they did. But then I added a reference to ToG into Transmute and from there came Polymute!