User blog comment:Digdux/Basic Design Phantomenia/@comment-7345250-20151201211454/@comment-7345250-20151201213513

Gotcha.

And one more thing. This RP started a few months before the FIENDship comics were even announced, so we've changed the changelings' origins a little to fit the lore. Queen Chrysalis is not the first queen of the changeling horde. It was actually one of her ancestors who emerged from the tree. Chrysalis just talks as though she was the first queen to scare her enemies, defend her authority, and stroke her own ego.

In other words, the story she told Twilight Sparkle in the comic was a corrupted myth of the actual birth of changelingkind.