For Associated Items column we need to be able to quickly fetch the relevant child items for each parent, so you can create advanced forms with repeating tables. When you have a limited numbr of items, it is not an issue, the query will be perfomed very fast. But as your list grows, SharePoint will have a hard time retrieving the child items for the particular parent among thousand of items in the child list.
This is where indexing can help. When you configure indexed columns, SharePoint is able to perform queries on those columns much quicker. What more, once you reach the throttling threshold of the list, all queries are blocked. Unless you are using indexed columns!
Until now, users had to configure the indexes on their own, which was not very convenient. Now, we added automatic index management mechanism. Whenever you create a new Associated Items column or update an existing one, we will ensure that the column we use for fetching items are properly indexed.
Note: this feature is already available on Office 365. Our on-premises customers will receive the feature in the next release.