Firstly, in terms of the game engine mechanics, are starbases limited to just one type/class of starbase per race?
No, but you might need to have different construction ships for each starbase.
Secondly, if not, is the game engine capable of handling an entity metamorphisis?
What exactly do you mean by that?
Finally, can a buildable entity be limited to specific area or terrain, like starting homeworld or terran worlds only?
Uh, depends what you want to do. You can indirectly do this by A. Making the building unbuildable, but spawn them in at the beginning of the game for things like homeworlds, or if you just want a unique structure you could make them captureable. If you really want the structure to be buildable, you can B. make it require so many tactical/logistics slots that only one type of planet could support it, but that is a bit crude.
The idea I'm toying with is using the current starbase template within the game as a flexable/multi role 'outpost', while being able to upgrade it to a ristricted role stationary starbase by using multiply contructor ships to upgrade it through multi phase contruction events (probaly 4 or 5 construction phases), much like the research process for titans.
Hmm, how different are these things? You can only really change how a given starbase looks through the regular starbase upgrades or research, you can't really induce a change via an ability from another ship. You could do things like double its weapons damage with other constructor ships though.
Really you'll probably just have to play around with it yourself, much of Sins modding is figuring out how to get your general goal to fit with what the game can do. It will almost never turn out exactly how you envision it in your head (until you're one of us olde veterans who already know the limitations through painful experience ), but I think you can get close enough with this.