Yes, it will cover trunk and side bags. I have the copy of the Givi sized for two helmets - 37L size maybe?
Mine lives in a garage now. However, for outside use you may want to get some of those clips you can attach anywhere to tarps. This will give you additional points to secure the cover if it is kept in a potentially windy area. Most covers only have one securing point at the bottom. I like to add one thru the rear wheel.
Sun is more of the enemy than rain as the bikes get older.