Lithium metal batteries are a bit more dangerous, as the lithium can (will) burn if it gets in touch with humidity (even air humidity). For the more common lithium-ion batteries the main concern is that it's very easy to short the contacts (as they are usually on the same side of the battery) if the spare battery is loose in your luggage. The short can create a fire. This is much worse if it happens in the storage bay than if it happens in your pocket inside the cabin.