“Matrix is also the name of a company and communication protocol of the same name, which has nothing to do with the crypto communication service Matrix.”
It seems it's a separate thing from matrix.org, though if I was to guess maybe it's using the same software stack?
What steers me away from them using the same stack as matrix.org is that a compromised matrix.org server (only backend, if you control the element web frontend you can trivially get access to what's displayed there) still doesn't lead to compromise of messages, so it's either that the server compromise led to finding guys and having them unlock their phones, or it's actually a different stack.