In VV1 and VV2 you could get a villager to honour the dead by taking them to the gravestones.
Like others it is the first few to die I miss the most.
I cannot make them do this in VV3 although some do it spontaneously, they go to the flowers by the fountain.
Is there a way to get them to honour the dead I have not found?
I liked that in VV1 and 2 as well. Sometimes in VV3 if you get them to read the roster then they do it but this might just be coincidence. Let me know if it works for you.
Secondly. All my villagers that die are seen as the bones on the amphitheatre.
Is that case for everyone?
Yeah, mine do it too. It's kinda sweet that they go to the most sacred space to pass over though.
I hope this helps.

Blessings
Magicangel