I always hesitate to answer this question since crime is so random and unpredictable. We have left luggage in our car on many occasions (all tucked away and out of sight) and never had any problem. We left our car for 3 nights in the Orvieto parking lot by the train station and had no problems. (The only difference between you and us was we had nothing in the trunk...but a thief doesn't know that so the risk of being broken in to is the same) A couple of things we do:
We never leave anything out in the part of the car you can see (other than a newspaper or something) All maps, travel guides, etc are in the trunk.
We actually leave the glove compartment and any other "doors" open to show there is nothing worth stealing in them. (Not for a short stop, but if we are leaving the car for multiple nights)
We never get into the trunk once we park. Once we load up the trunk in the morning, we try not open it again until evening. (everything we need for day has already been packed in the day bag) If we do need to get into the trunk, we pull over and do it before we are close the parking lot.
People do get broken into and if there is stuff in the trunk it will be gone. (Thieves don't go through your stuff looking for valuables, they just take everything) Keep all your valuables in your money belt.
I would do just what you are planning.