Cubivore was an Intelligent Systems game and published by Nintendo in Japan, the fact that Atlus published it in the US doesn't mean its not a first/second party game. And while the GCN didn't lack Japanese support (or western support either for the first few years) its impossible to deny that the PS2 didn't dominate that generation so much that third parties often just didn't bother with cube or Xbox ports.
Physical region locking is still region locking, N64 and SNES are both considered to be region locked- nobody back in the day was paying people to mod their consoles to remove the divots or, if in Europe,/Japan, ripping all of their carts apart for that sweet Madden goodness.