Seconding what some others have already said, picking up a rental car as you leave Venice does make sense, especially if you'll be picking up a rental car anyway. If you took the train, you'd have to connect through Florence, which would add to the travel time.
The traffic-limited zones, with traffic cameras and associated fines, as far as I know, are limited to the big cities, such as Florence. I don't think Siena has such a system, and I know that San Gimignano does not, though you're not supposed to drive into San G. San G. is so small, however, that you don't need to drive INTO the town, though you can do so, to drop your bags if you're staying at a hotel in the town.
We like staying in towns, so we can have a wide variety of restaurant choices for dinner, and not have to worry about driving after dinner. San Gimignano is great at night, because the day-trippers have left and the town gets quite (but not too) quiet. We've stayed at, on different trips, Hotel La Cisterna and Bel Soggiorno. At each place, we had a room with a balcony overlooking the landscape, which was lovely. San G. has a greater number than usual of great restaurants, for a town of its size. When staying in San G., we park in one of the numerous parking lots right outside the town wals, and walk in from there. In April, you shouldn't really have a problem with crowds.
You will not lack for great places to photograph, but my favorite thing during our last visit to San G. was the path that runs entirely around the outside of the town walls. I went for an early-morning run along that path, and a little ways outside of town, and the mist rising from the hills stretching out to the horizon was magnificent.
Also, a number of photographers (including my husband) made early-morning visits to the tower in San G. that you can climb, to take photos there.
Enjoy!
