The primary use-case is to detect the dynamically defined indexes (by Command Rule), which will affect the mask process.
You need to remember that information about schema is static (It's not refreshing when the schema changes). Because of that, you can't mask tables which don't have a primary or unique key. In a highly distributed system usually, you don't put constraints on your schema, because it slows down the insert process. At the same time, you don't want to change your existing schema just for masking purposes. You can also use it for performance reasons. You can create an index on column which you will mask, so it will affect how fast data can be fetched and processed.
Moreover, The New Index Refresh Rule will refresh any Index manager inside of the controller with all available indexes to the selected schema from the controller. The position of the Index manager doesn't matter in the hierarchy of the controller.

Example of the main use-case:

You would like to mask the column Name in this table:

CREATE TABLE Customer (
Id INT NOT NULL,
Name NVARCHAR(255)
)

To create a New Index Refresh Rule, click new rule in Rules in the Set tab. You will get this window: