Reformat the Ad Structure.
Content obtrusive ads are bad for live form content. They work for YouTube and Television where the content can be put on a break until the advertisement is done, however for Twitch the ads will often block important content especially when first joining a stream.
Pre-roll ads need to use unobtrusive forms of advertisement. Since pre-roll ads are the only ads forced to run without authorization from the streamer, they are the ads that most likely will directly affect viewing content the streamer does not want you to miss. As a result these ads will discourage viewers from watching, especially when having to click through streamers to see exactly what is going on with their content.
The pop out window for the stream when an obtrusive ad is being played is extremely small, having an alternative viewer for this would be greatly appreciated. This could include allowing for use of multiple monitors if available, or an alternative viewer like full screen and theater modes which allow for the ad remain large but give a larger section of screen real estate to the stream as well. These should be optional toggles.