If you buy them at home you don't have to worry about stamping them that is one good thing.
The conductor will scan the QR code on the e-ticket. It definitely makes things easier more organized when you are not familiar with a place. No need to stand in line to buy a ticket or at the kiosk looking over your shoulder to make sure no one is trying to put a hand in your pocket. All you need to do is look at the screen to see what platform your train is going to be on. Cut out the steps you need to take from the comfort of your home before you travel, that's my motto. Just remember to print that stuff out before you go but keep in mind most hotels can do that for you if need be as the tickets come as PDF file attached in your email when you buy it.
I always buy in advance the more complicated stuff or to towns that I intend to use as a base to explore other towns. For example I bought my train ticket from the airport when I got to Rome last January. I bought my ticket to Pisa when I got to my base in Monterosso al mare. I was in Perugia last July 3 days and bought my day trip ticket to Assissi.
The Duomo is the highlight of Siena. After you see enough medieval towns they all start to look about the same to me no matter what country but there is always one building that tops it and the Duomo there is it. But unfortunately there are the human traffic jams
Actually I did not stay in Pisa which I found good as a day trip. To me It was worth an hour after you see the tower.
Corniglia? It is just part of visiting the whole Cinque Terre which is great especially the hike from Monterosso to Vernazza.
I did not do any ferries. I actually stayed in Monterosso al mare which is about a ten minute train ride or 3 hour scenic hike to Corniglia.