Last point ... instead of forcing the larger molding to fit the wavy floor, the historic solution is to add another course of shoe molding. Just nail your larger, thicker molding as level as you can. Then, add the smaller, more flexible, molding to the bottom.
You can also add a similar molding to the top in lieu of a thick caulk line. Then you will be left with a much thinner caulk line on top and no gap at the bottom.