The rules state I can spawn in a cryopod for every creature on the island (a total of 88) as well as a vault to store them in. Am I able to use these cryopods throughout as tools rather than just for storing the dinos I need for the list? Like if I want to transport a land mount to the carnivore island, may I use a cryopod to transport said dino after swimming on an ichthy? The rules don't state any restrictions with these spawned cryopods.

you are free to use for everything, however if you need more (or lose) cryopods you have to craft them.