Hey Will, found your article while debugging my own project using this approach in a collection view. My conclusion is to refactor this into a tableView but wondering if you ever encountered this weird behaviour before and if there's an easy fix.
Essentially calling performBatchUpdates on the collection view in order to animate some layout change causes the hostedView to disappear from the contentView.
https://github.com/ahmad-earnin/ViewControllerInCell-Example/tree/collectionView