The thing about pausing and leaving the game running, is that it doesn't stop aging. This might cause some inconsistencies that cause the game to shift the bones over. Have you ever had them collect a body from a death that occurred while the game was running? Do you know this to happen when a villager dies while the game is running normally?

I never bothered to look at it much, but I've never seen a death that happened when I was actually there. (I never played VV marathons, as you can probably tell.)

Oh, and no, I don't know of any way to manually 'honor the dead.'