Best one day rental car parking option - Villa Costanza or Train Station?

Do you have to be in Pietraviva that day? Spending a night in Florence and leaving fresh in the morning would be my choice.
I would have major qualms about leaving luggage in a car unless you can find a place where a guard is confirmed.
Although an hour drive on arrival is within the "done it" zone for me, I have found that delaying the drive in any way drastically increases the chances of jet lag taking over on the drive.

We were in Tuscany last month and parked at the big Villa Costanza lot right off the A1 and it was great. Easy access in and out, Tram 1 ran about every 5 minutes and took us right to SMN station. Even if you get an SUV it will probably have a pull-out cover in the back to hide your luggage. Good luck!

I would visit Firenze before picking up the car, and, as Valadelphia said, I'd go to Pietraviva the next day, if you can. I wouldn't drive there after a long overnight flight (I presume you arrive from North America). The road is largely freeway, but the last portion is a narrow two lane highway between Levane and Pietraviva (I've been to Ambra many times since I friend of mine had a country house there) and after a long flight and a long day touring the city, you will be tired.

Also Villa Costanza parking lot has been plagued by constant car break-ins so I wouldn't leave the car there with luggage inside. I know last December the City finally decided to have more security cameras surveilling the place, but the lot is unguarded by humans except for the occasional patrols, so security cameras are not necessarily a panacea.

Do you have to be in Pietraviva that day? Spending a night in Florence and leaving fresh in the morning would be my choice.
I would have major qualms about leaving luggage in a car unless you can find a place where a guard is confirmed.
Although an hour drive on arrival is within the "done it" zone for me, I have found that delaying the drive in any way drastically increases the chances of jet lag taking over on the drive.

Yes, it's for my cousins wedding and he has rented a villa for all of the families and that's the first night we are all getting together.

We are flying to Paris first for a week, so we will be flying from CDG to FLR and won't be too tired to start the day.

Great--I wish we had that pertinent information to start with!
So, I would go with #2. When you rent a car, you provide the pick-up time, so although things can certainly go awry, I would book with confidence.

PS Don't think a trunk guarantees your belongings--it is just a psychic reassurance, a thief can pop a trunk in seconds.

We were in Tuscany last month and parked at the big Villa Costanza lot right off the A1 and it was great. Easy access in and out, Tram 1 ran about every 5 minutes and took us right to SMN station. Even if you get an SUV it will probably have a pull-out cover in the back to hide your luggage. Good luck!

did the lot feel safe? This seems like the easiest option, i just don't know how safe the lot will feel.

Feelings don't mean anything, facts do, and facts say that break ins at Villa Costanza happen, and not infrequently.
A safer alternative would be to park near the airport at a safer guarded car park. These are some options
This one is in front of the T2 Tramway stop
https://maps.app.goo.gl/E3dV7zFh5Bfg3oPj9
This one is also nearby the airport. It is the parking garage of the Hall of Justice of Florence, so plenty of security cameras. If I were a thief I wouldn't break into a car in the garage under the Hall of Justice, too much police around, although you are there on a Sunday. The T2 tramway stop is 5 min walk
https://maps.app.goo.gl/BtnsQtd1MW1TiAJs6.
I presume you could also use Bounce bags or similar service at the airport, and pick up later before getting the rental car at the airport rental center.