I would not do the twist and rail set for a 3 yo. My DS got it at 5, I wouldn't do it before that.
He got the basic set at 3yo, it was perfect for that age:
http://www.amazon.com/Manhattan-QD80.../dp/B003TI4R9A
For the bigger set, I do agree that bumping it is a problem. We set it up on the coffee table and it's reasonably stable - can survive a week or so with DS2 (3yo) around, but he knows not to really mess with it and how to put the marbles in carefully. I think our set up - on a wood table on a wood floor - may be a real factor in our success with not having too many crashes. The one at the toy store is probably glued together. Good choice for a toy store, takes the fun out of it at home.