At the moment, the TwoColConflict extension does not interfere with the new Wikitext editor. When using the two column conflict solution screen, while having the new wiki text mode beta feature enabled, the screen show the "normal" source editor.
But that seems also to be the case for the default edit conflict view. With the new wiki text mode enabled on a edit conflict page I get the "normal" editor. I can only assume, that this is intended. But would be interesting to know why and also what would happen to "our" editor in the two column view, when they enable their editor on conflict pages.