The problem is that wikiEditor is initialised twice, once in ext.wikiEditor.js without a toolbar, and once in ext.wikiEditor.toolbar.js with a toolbar. Previously these happened in one clock cycle despite both being wrapped document.ready calls ( $(fn) ), but I imagine this has changed with jQuery's changes to already resolved promises being async.
Having discussed with @Catrope and @TrevorParscal (the original authors) I think the best approach is to get rid of some of WikiEditor's modularity. The toolbar is essential to using the editor so should be merged into core. The dialog module is enabled by default, and making is disable-able servers no real purpose so enable that always too.
This will allow us to remove the empty initialisation and rely on the toolbar initialisation to load the editor.
It seems that this remove everything from the non-dialogs mode, but still actually 'goes' through the non-dialogs mode during setup, as described in T166857: The globe in WikiEditor disappears when loading is finished. I think that was an oversight...