Some of the differences between favorite listings and pins will be changed by our next app update, v1.3 which will be available in about 2 weeks. In particular they will both show for low zoom levels, pins will be easier to create and move, and pins will offer more customization (selectable icons, color, etc).
The main difference though, and the reason we show them in separate lists, is that Pins are generally used for marking locations of personal interest such as your home, work office, friends houses, favorite hiking spots which never have listings for them, etc. Its true that the maps are often lacking POI listings for some of the places you frequent and so creating a Pin to represent them is convenient.
We will consider allowing Pins to be placed with the My Listings for one of our future updates, or ideally we would allow users to submit new POI to the OpenStreetMap project so that other users will be able to see them on the map too. For now though it is possible for anyone to add new POIs to the maps through the OSM website. After adding data there, it will appear in PocketEarth after the next data update which happens every few weeks.