I had a cockpit only cover but subsequently bought one that covers the bonnet as well following a situation where rain got under the bonnet, through the firewall and into the ECU. Would highly recommend them when away from home.
I agree. A tonneau serves it's purpose in a light summer shower but for a storm cover I can see no point in other than a full one.
Never had any paint chaffing issues with mine as although it's light it's multiple layers provide enough stiffness to avoid flapping in most winds.