Hi Mon,
You are right that visibility will affect all keyframes since it's not a property that can be animated. You can add a timeline event to turn the visibility of the youtube component to hidden when getting to that time. Here is what you can do.
1. Switch the timeline to advanced mode (to see the layers instead of the big thumbnails) by clicking on the icon on the right side of the timeline.
2. In the Events layer at the top, right click on the time where the youtube video is supposed to fade out and select Add event.
3. Double click on the event marker to open the Events dialog.
4. For Actions, select CSS > Set styles.
5. Select the youtube video as the target.
6. In Configuration, click on Add Property and type visibility:hidden and press Enter.
7. Click OK to save.
Hope it helps.