The audio will not be heard and the video will be jumpy (lower frame rate).
You should use the Share A Video feature.
https://support.goto.com/webinar/help/share-a-video-beta-g2w090120
With this you need to stop the PowerPoint, show the video, then go back to the PowerPoint. It takes a little practice doing this. There is a limit of 5 videos for a single webinar. Both the visual and audio quality is very good with this process.
If you are using a Mac, here is a solution I use.
https://community.logmein.com/t5/GoToWebinar-Discussions/Play-video-embedded-in-PowerPoint-and-mix-m...
One drawback with this is that if there is music in your video, it will sound bad. Also if the voice in the video has not been "mastered," you might not hear the quieter dialog.
