I was under the assumption that WordPress is OSS, and WPEngine is running this software on their platform, so there was an update to this software, contributed by Automattic developers which included a banner denouncing WPE, and the WPE people decided to just deploy that update to their platform?
I don't think that means they "put the banner on their instance" does it? If they are unhappy with the management of the open source software they are using on their platform they presumably could fork it, or decide to not deploy the version that includes this banner, no?