PNG Dungeons is a deprecated thing. Chucklefish didn't disable it, because they don't want to redo their old dungeons. But Tiled is more versatile, and it let you have a deeper level of customization.
Seconding @GonDragon. Tiled is generally better. One thing I wished Tiled have though: the ability to find objects by its in-game ID name. It's kind of frustrating having to check the tiled folder to find out an object's Tiled ID Number - so we know where is that darned chair is sorted. With PNG you only need to write "apexcoolchair" (the name can easily be found in the Starbound wiki) and it's all set.