It won't hurt. The more media the more room for bacteria to grow, the more carbon to help clean the water. Part of the reason for the extra slot will depend on how old the filter is. This is a company that makes regular changes to their filters every few years in an attempt to improve them and keep up with the newer competition on the market.
Something that works good in that extra spot is a sponge. Many of the sponge inserts they make for the Whisper filters by tetra will fit into the Penguin filters. This is cheaper for the consumer, collects bacteria without needing to be changed monthly, so preserves the culture better, and when it gets dirty, simply wash it in dirty tank water during a water change, and put it back in. Just be sure not to rinse filter media under tap water and then put it back in. The chlorine in tap water will kill the bacteria culture, which makes the use of a sponge pointless.