In the facilities portion of the construction screen, I see two resupply depots. They seem to be identical. Is this just an unintentional duplication, or is there a difference?
I think that is a typo in the facility file.
It gave me a "system wide" warning which seemed silly to me since there is a lot more to the C.C. than its system wide abilities,
Any duplicate system-wide ability gives that message.
But does this mean I can't build it at all or does the time exceed some display limit?
The build time does indeed exceed the display limit. You could conceivably leave a book on the f12 key for a few weeks and see the CC get built.
Does the "Colonial Community" have any special properties or is it just a multi-function facility much like the monolith?
It is a lesser City facility. The Cities are the big resource facilities, like mini-CC.
"Agrarian Colonization". I have no idea when or why I would use this. Any hints?
On a planet with 100% organics value and really poor minerals and radioactives values.
"Colonial Development" and "Large Support Facilities". Are these really just for the AI, or should I be researching them anyway?
I think those are there so that the AI doesn't try to build these types of buildings. You should definitely research them.