My favorite spot is also in the val d’orcia/crete senesi region.
Been to Tuscany twice, it’s an amazing region
I was in a fantastic agriturismo very close to buonconvento
http://www.agriturismopoderecunina.com/en
Amazing place, raving reviews, fantastic hosts.
The road, sp146 from san quirico d’orcia, going to pienza, Montepulciano. Then south to la foce, montichiello and back to san quirico is the best of what tuscany can offer.
As for the car, logical to take your car when leaving florence, but when done, you’re going to Rome? Why don’t you drive there, you can stop in Orvieto, you’ll see an amazing village and one of the most impressive cathedral in all Italy. Then just bring the car to probably the termini station where all of the rental companies are, unless you can find somewhere close to your appartment.
As far as medieval towns, the not-to miss would be montepulciano, pienza, san gimignano(do it very early morning or after 4:30 to avoid to feel in a tourist trap). It is a gorgeous village when it’s almost empty. Volterra, sienna for a full day. Montalcino’s fortress is a great place to take spectacular pictures of the surroundings as you can walk on top. Very close the amazing sant antimo abbey. If you have enough time, monte oliveto magiorre is also a great visit. San galgano abbey makes fantastic pictures but is 1 hour west roughly. Perugia in umbria, 1:30 from buonconvento, also has a fantastic piazza, great museum, etc.
You can also think of a one day trip from Florence that would bring to pisa and lucca.