Oliver Hazard Perry leader counter from Amateurs, To Arms! by Clash of Arms Games.
Warrior Band counter for Conquest of Paradise by GMT Games.
Are both part of the island connected (scoring), when there is transport canoe chain at one of them and there are troops/villages at both.
Common sense would say yes, but this is also board game and no rule actually says so.
The answer is yes and actually, the rules DO say so. The start of the fifth paragraph of The South Island advanced rule (page 10) says: "Te Waka Maui acts like any other Island Group in all ways, except one." The one exception is how Colonies and Warrior Bands can walk between the two island groups without canoes.
So yes, Aotearoa and Te Waka Maui each score the VP for Controlled Island Groups if they're connected by Transport Canoe Chain. When the rules say the South Island acts like any other Island Group in all ways, that's exactly what it means, including VP scoring.