I'm pretty convinced there was supposed to be a cut scene with Kain that was never finished/completed.
That's one possibility I hadn't considered. I was trying to think of some place where it could be located, if it was supposed to be its own playable map, and the only thing I came up with was that useless chocobo forest on the island between Troia and Kaipo. Me, personally though, I kind of assume that was the original location of the chocobo's village, since it's so much larger than any of the other forests, with the exception of the one south of Troia. This place could could've been there, too, I suppose.
The After Years has a few forested groves like this scattered about the map, which contain treasure. Maybe something similar was planned for this area, but there is no chest or tall grass in the playable area.
I had a theory that that the "useless" village on the island was supposed to be the Chocobo Village with the Black Chocobos so you would have to really search the map looking for it rather than it being north of Troia. It kind of makes sense, only Chocobos that could fly would be capable of making a village there. That and it's close enough to Troia to make sense that they "found" black Chocobos there. My guess would be that it might not have been done and/or removed because play testing found it to be too difficult? Or maybe it's just a canard while you look for the actual Black Chocobo villiage/ I can't prove it but it seems to explain the otherwise useless village as you've aptly dubbed it.

That would be a cool hack actually. Move the black chocobo village to that island so that an experienced player would be thrown off by the change and have to actually go looking for it when doing the earth crystal / dark elf / Zot arc... I like it!
Yup...works like a champ...
(In v1.0 FFII ROM) Modify world map triggers at (headered) offsets
0xD017E (Island Chocobo Forest) = 564F21081E
0xD0183 (Troia North Chocobo Forest) = 2935D4081B
Then Modify Event #0x75 @ 92CF6 = F00DD8FEFB564F02FF (This is important as the line "FEFB564F" modifies where the Black Chocobo takes off from and sets where it returns too. Failure to change this event will likely strand you w/o a way to get back to your airship!)
And there 'tis...

...Of course you could just put the black chocobos
anywhere including somewhere they shouldn't be early on in the game so you can go places you shouldn't be...