Yes it must have humpback whales on-board or else it makes no sense to me
You have solved the mystery. However, why not release the whales into the open ocean instead of in a bay? TBH I put the BoP landing in SF Bay down to Spocks calculations which ofc he gets 100% spot on. He wanted to come down right infront of that window at the precise moment Sarek is looking out and furthermore Spock wrote these calculations on the back of a napkin! Spock fucking rules.