Flooring transitions help (w/ pics)
Your first pictures is a little confusing (hard to tell by the picture also). Is that a long gap next to the wall wider than the doorway? I'm assuming the flooring isn't finished and you're going to rip a piece of wood to fill this space, correct? Regarding your question about the T molding, I wouldn't worry where exactly the T molding falls, it should look fine being under a door or anywhere in the threshold.
Your second picture is a tough one, and I'm not sure what's "best" to do. What's easier is surely to just put a T moulding over the marble and hardwood, but probably the "best" thing (cosmetically at least) would've been to tear out the marble threshold, install the wood flooring closer to the doorway, and reinstall some kind of threshold? Hard to say..