Whilst chunks can be unmarked when item is destroyed in the end, chunks are not marked when the item is put down.

They are, if the message doesn't show when you place a block that is because something else {possibly another CNGBB block} is already loading the chunk.
Notice how there are no xp orbs in the chunk i'm in, that is because there is a chunk loader in it and they timed out while the others were unloaded.