Transition piece first or baseboard first?
I would imagine it's a matter of preference, but IMO the transition is part of the floor and the baseboard is part of the wall.  Given that the transition will blend in with the floor, I'd be inclined to put the baseboards on first and then cut the transition to fit.  It's also generally simpler to cut something to length than it is to notch something cleanly and precisely.  

Ultimately I don't think there are any severe consequences for doing it one way rather than another.