Appropriately, BlackWater Canyon is one of the most barren areas of Dinosaur Planet, though this is due to fluctuations of development rather than the grave setting. 

While the entirety of the Canyon can be explored, all associated programming with the area is completely absent, meaning that interactions with the ShadowHunter Tribe, the intended boss fight, and any narrative elements to be imparted within BlackWater Canyon simply do not exist at this time. 

NPC's: 

Shadowhunter Leader: Envisioned to give Krystal the SpellStone, as the areas intended SpellStone Guardian. 
Shadowhunter Thief: Envisioned to steal the SpellStone, prompting a chase throughout the Canyon to the boss.

Key Items:

BlackWater Canyon SpellStone: Needed to return to Desert Force Point Temple for progress in Krystal's Adventure.

N/A

Moon Mountain Pass Key Bug: Chief Lightfoot may not appear to give Key, despite having met all requirements. 
Status: Manageable.
Solution: Restarting the game and resuming Krystal's Adventure, or adding the Key to inventory using a code.
 

SwapStone Circle is one of the most stable areas in Dinosaur Planet, and despite the Totem Pole puzzle being incomplete, does not pose any outward problems towards completion of the game. 

While SwapStone Hollow would appear in Starfox Adventures as ThornTail Hollow, SwapStone Circle was made redundant by Krystal's removal, and cannot be found in the GameCube adventure in any capacity.