I'd suggest to not do anything here. If you do not present content initially, the expected user experience is that focus shuts off again and only becomes active again when the user interacts with it.
Agreed, my intent was simply to customize the behavior of the focus engine very slightly in order to create a consistent experience; as the collection view is in fact populated in less than a second from showing its VC (this includes the animation from UICollectionViewDiffableDataSource.apply(_:animatingDifferences:completion:)), it is a bit jarring to sometimes have the focus moved to the correct item and sometimes not.
UICollectionView and UITableView have delegate methods for the preferred focused index path that will be used
Here I would like to suggest a clarification for the docs - collectionView(_:shouldUpdateFocusIn:) and indexPathForPreferredFocusedView(in:) only seem to be called for focus movements that occur after the UICollectionView first receives focus. This was not clear initially and was a pain to work around, as we need the custom behavior from those two methods even upon the first focus request since starting the app (e.g. to be able to focus the first item that is completely visible and does not intersect a sticky header after scrolling). This might have something to do with being in focus deferral mode, of course.
Thank you for your help on this topic and please feel free to challenge any incorrect statements I've made - at the moment I only have empirical knowledge on focus quirks.