Same DDR3 total capacity, different chip capacity configuration, speed different?
Faster in what way?

Configuration 1 will give double the memory bandwidth since you are accessing 32 bits at a time (assuming you have a 32 bit wide memory controller).

But depending on what you are doing raw bandwidth isn't always the biggest issue. Latency is often the real performance killer since that's how long the CPU has to sit around waiting when it has a cache miss. 
Latency for a 16 bit memory access will be the same for both configurations. For a 32 bit memory access configuration 1 will be a little faster but not by a massive margin.

So yes, configuration 1 will be faster. How much faster will depend on the CPU, memory controller and memory access characteristics of the end application. It could be almost twice as fast or faster by such a small amount it's not noticeable.