You will use your account password to log into Pocket Geek ID.
You will use your Master Key to retrieve and access protected data (like your passwords). Your protected data cannot be retrieved or accessed without decrypting it. The Master Key ensures that you and only you will have access to your protected data.
Your Master Key is not stored by Pocket Geek ID, so there is no way anyone can get access to it unless you give it to them. Your login password needs to be stored somewhere, so if your Master Key is the same as your login password it might be guessed if anyone ever managed to gain access to your login password, therefore removing the strongest layer of protection for your sensitive data.