If I had a choice, I would choose a trunk. If not, there will be a cover that looks like a rolling window shade to cover the bags. My concern is, with the cover extended, it's obvious that you have something in the car.
Regardless of which you end up with, use some care where you park. We skipped parking near the train station in La Spezia because the lot had lots of broken glass and questionable people milling about. I chose to park near the navy base and walk back to the station.
Keep in mind, it will probably have plenty of room for two carry-on bags. If you're carrying two 26" wheeled bags, however, they probably won't fit below the cover. Trunks aren't much bigger - pack light.