If you update to the latest beta (https://www.displayfusion.com/Download/Beta), the Window Location feature has been replaced by the "Triggers" feature. It will import your existing Window Location rules, and then you can edit the one for Chrome, and have it exclude a certain Window Class. Just open a YouTube video and make it full screen, then use the picker (the little target icon) next to the Window Class field in the Trigger rule to pick the YouTube window. Add a minus sign "-" in front of the Window Class, and that should force DF to ignore the YouTube windows when processing the rule

Hope that helps!