Is that caulk, or did you put another piece of wood underneath?
For the shoe molding that goes past the transition piece (part that goes over the gap between wood/tile) I would consider putting the shoe molding in first, then running the transition piece up to the shoe molding. Either way, you may have to caulk and paint to fill any gaps, but if you butt the transition to the shoe, it may look pretty good...
Hack (a.k.a. Jeff)