Every metaroom in C3/DS occupies a position in the world, although their locations do not necessarily reflect where they "should" go--the Creatures 3 environments are all arranged in a rough rectangle while the "main" part of the ship is just below them. The placement of third party metarooms is left entirely up to the creator. A map of most of the metarooms can be found at the Norngarden website.
It seems that the original world is mostly full, though there are a few gaps for small metarooms. However some creators have succeeded in increasing the map size to encompass much more space, about 50 to 100 times as much. There may be some compatibility issues with this larger world but if there are, they are not known. A list of Creatures 3 and Docking Station metaroom coordinates is maintained on the Creatures Wiki.