We visited Florence for three days in 2019 as independent travelers (family of 4).
We spent 2 days in Florence and the 3rd day we took this exact bus tour with the company below. The company has many other tours.
https://www.ciaoflorence.it/en/tour-detail/13
From going on the bus tour, they told us that if we got lost from the bus tour, the tour company home office could help us get back to Florence from Siena by train. So my guess is, it's pretty easy to go to and from Siena on your own. The bus tour left from the back of the main Florence train station.
We stayed at the Hotel Torre Guelfa. It's quirky and not deluxe but cool anyway. It has an antique breakfast room and a rooftop view that hotel guests can make use of. Rick Steves recommended it. In good weather you can walk to it from the train station. It's close to the historic center of Florence, near everything.
https://www.hoteltorreguelfa.com/
I felt a lot of the AirBnB's I saw listed for Florence were sketchy. My husband and I don't like to drive overseas unless it's impossible to get around. The one day bus tour of 3 cities saved us a lot of cost and hassle. You might feel the same.
Enjoy trip planning.