It seems like content that appears in the top stories section may be deduplicated (removed) from the main search results if the top stories box appears before the main search results listings and the listing is the first link in the Top Stories. This is according to Danny Sullivan from Google, after Deiter Bohn, the executive director of Verge, has called out Google about search listings that were stealing content from The Verge.
Deduplication or the removal of a listing from the search results, if it showed up in a featured snippet or top stories, is nothing new.
In January 2020, Google started deduplicating the featured snippet, which used to be in the right sidebar and migrated it into the main search results column. Before that, a result could be displayed twice in the search results – in the featured snippet, and in the main results page.
According to Sullivan, deduplication can often be useful, it gives more variety for other publications or other search listings.
There seems to be some mix up though as there are some listings that were not deduplicated.
Barry Schwartz of Search Engine Roundtable did a search to check on some listings and the deduplication that happens. It seems that it varies. There are some instances that Google did remove top story content from the main search results. There were also times the top stories were not deduplicated from the main search results and showed up twice.
More details of this are in this SERoundtable article on deduplication.
So it seems like it is not exactly clear when Google might be deduplicating content and when it is not.