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A shorter better way of summarizing this bug:
CollectionEntry::postInitialize() assumes that it's taking a snapshot of the pristine collection.
However, anything descended from AbstractPersistentCollection will apply writes during afterInitialize(), meaning that by the time CollectionEntry::postInitialize() is called, the collection is no longer pristine.
I'm digging through tickets and code trying to find some indication of which assumption "should" be right, but without much success.
Alternately I might be misunderstanding the purpose of the CollectionEntry snapshot. Should the CollectionEntry::snapshot include queued actions? If so, then the bug would be that routines processing the snapshot can't handle transient items.
What is the purpose of queuing actions in the first place?