There are some feature in matrix that flights didn't pick up. The original matrix site was even more powerful and exposed some operator-ishness, depending on what kind of account you were granted.
I suspect that branding is powerful, so it's better to keep an existing flight search running than to axe it in favor of something else and loose all the existing customers. Google bought ITA and kept matrix.itasoftware.com running with (presumably) the same branding; Booking Holdings bought Kayak and kept kayak.com running with the same branding.