Are you running the infrastructure? If push notifications go from your Matrix server to some server run by Element to Apple to your phone then Element is subsidizing you.
Yeah, but everything else being equal (using Element), I have my account on their server too, and use push messages there. Or I only use their push messages and host my own server. As far as I understand both are free.
So you have nothing to worry about, then. If you were running your own Matrix server, and wanted to use their push infrastructure.. Well you're still fine for now but who knows in the future.