Travel in Italy

Frankly, the distance between Venezia and Florence is only 3 hours by train, same case for Florence and Rome. From Florence to Pisa is only 1 hour by train. So, you don't need to travel by air. It helps nothing, or even it will waste more time. Plus Italian railway is well developed, so railway is the best option in your case
Since the distance bewteen cities are not big, there is almost no night train service. You can take a train departing at 9:00, then you will arrive your destination at noon. There is no comparision so we cannot say which one is better. But the train in Italy is safe, but please pay attention for your personal belongings.
Please forget the railpass, train service is quite cheap in Italy. Venezia to Firenze is only 40 euro (Eurostar Italia), same case for Firenze to Roma. Florence to Pisa costs you only 15 - 20 euro. If you take ordinary EC or IC train, cost will be lower. But a railpass costs you at least 100 euro. It's much expensive than single ticket.
You don't need to bo0k ticket in Hong Kong. Train service are extremely frequent bewteen cities you have mentioned. You can buy ticket after you arrive Italy. Trains operated between these cities hourly, or even twice an hour. If you miss one train, just need to wait for a short time, not a big deal !!

personally if you want to travel to another city overnight, railway would be my #1 choice. But if you can't sleep on the train or some other problems, flight would be the best (see easyjet or ryanair). you will then have to get your railway pass in Hong Kong. About the ptp or travel pass question, you will really need to do some homework to see which one's cheaper. (www.eurail.com)