Because the configuration in extension.json is merged with your config in $wgSiteMatrixSites, you can't actually remove any of the default options -- Wikipedia, Wiktionary, etc. If you're running another wiki farm, this situation is less than awesome. I could, of course, edit extension.json, but Miraheze likes to track upstream whenever possible.
If I'm wrong about this, please let me know how to remove a site from the matrix on top. Thanks!