For clarity, Element is merely a client (the main one) for Matrix.org. What matters is whether people are on Matrix rather than whether they use the Element client. But most Matrix users surely do use Element.
matrix.org is just one instance, it is very important that people choose different instances so that interoperability is kept.
I think the poster was referring to the protocol instead of the instance.
Maybe this was a case of user error but I know I was not the only person who had difficulty joining Mozilla's riot with their existing riot username when Mozilla first opened their server.