It was called css-layout but got renamed to Yoga because it implemented the “flexbox” layout and not all of CSS. Flex -> Yoga was indeed the joke/reference.

Here's another one: https://facebook.github.io/prophet/

It's used to predict things, but still strikes me as an odd name, just like Yoga.

The comment you're replying to is a perfectly good reason why it's named Yoga, not sure why it'd still seem "odd" with that context. Not particularly witty, but it definitely makes sense.