I don't have a tonneau yet. Started making one last year and it needs a bit of sewing. Will use it when i get it. BUT
I want to reassure you about your fear of leaving the car open to "sticky hands."
I live/work in Baltimore City, where street crime is pretty common, and there are a few 10s of thousands of active junkies out and about at any given time, most of them looking to score something to sell to buy their next fix. This is especially true in the upper reaches of downtown--again, where I've spent the majority of the past decade--owing to the homeless services providers and the city's jails being right there.
So if anyone is going to have trouble with "sticky fingers," you would think it'd be me.
And yet: Never in the many days I have parked Bridget in an unguarded surface parking lot, open to all and any, has anyone ever taken anything out of her.
Never lost the half-inch wrench I keep under the seat to adjust the windshield stanchions. Never lost any gloves, or sunscreen, or any change out of the door pockets. Never even lost the nippy flask I keep in the glove box.
Nippy flask!
My theory on this is two-fold, and one of these folds, I think, applies directly to your situation.
The first fold is ****-luck. Truly I've had it, in this aspect of my life at least.
The second, and more applicable fold, is respect.
Talking to people in all walks of life and in all neighborhoods around Baltimore, it is my experience that even habitual thieves, and even junkies, up to a point, would rather leave a car like mine or yours alone than reach in and grab. There is just something about a car that special that makes even these guys hesitate to mess with it, even if they're perfectly willing to smash the window of the 2011 GTI parked two paces away just to get the 78 cents they guess is in the console.
I know no one is immune, and surely your mileage may vary. But I really think there is something to this. So don't worry.