Twitch used to work without Flash on vanilla CEF up until about a week ago. It was already using something else than mp4 and i’m fairly certain that android/ios also use other codecs. The removal of Flash was about 2 years ago now and is not related.
I looked into it some more and the twitch player source code does indeed reference vp9, passes a feature check and is trying to load it. After that it encounters a bunch of errors related to chromecast not existing in CEF. Hard to really make conclusions without the original source but there is no indication of video codec problems.
edit: Those chromecast errors are also happening in a normal browser so probably not related.