Don't know anything about the buses. I can't resist sticking to boats when in La Serenissima. January is a great time to go to Venice. The NY Times did a nice pictorial about it. You can see it here:
http://www.nytimes.com/slideshow/201...128VENICE.html
I have to go to Venice every two or three months and have to stay for about a month. Last year I got to spend most of last winter there. It's so much better than going in the summer. Nothing like having the city in its natural state, not overrun with tourists. Nothing like walking in the cold mist, and dropping inside a warm barcaro for cicchetti. I don't know if you've been there during aqua alta. Be prepared to buy boots.
For your question, I don't know anything about the trains. I understand your reluctance about the bridges (Arsenale is such a great place to stay), but I always stay on the boats. As for when the ticket is activated, it is activated by the machine at the dock when you pick it up.
The value of the pass when picked up during off season, it is true, is a matter of a modest amount of euro's. During busy season buying it over the internet is the same cost at buying a ticket at the vaporetto stop. But the value is even greater. There are long, long lines at the ticket counters, with 20 to 40 people in front of you asking multiple questions. It's great to be able to just wave your pass and step on the boat. For museums, instead of waiting for two hours on a line to enter a museum, with the Venicecard, you get to go right to the front of the line. You won't have many lines to deal with, so the value to you will be a savings of $10-20 euros, depending on what you buy.