The Master List is a collection of all unique email addresses from all other lists in your account. A single email address may exist on two or more lists in your account but it will have a single entry in your Master List. As a result you may find the count of email address in your Master List is lower than the sum of email addresses in your other lists.
In addition, when deleting a list in your account you have the option of removing the addresses from all lists (including the Master List) in your account. It's also possible to delete a list but leave the addresses on the Master List. These two factors can account for differences in size between the Master List and other lists in your account.