I’m not sure what the mechanism for burying a town or city section is. It seems to have happened since antiquity, so it’s obviously the rational choice over millennia, but my intuition doesn’t connect. (Aside from soil deposits and erosion.)
For ancient archeological sites, burial happens when places get abandoned (typically due to war, or economic reasons, or famine). A lot of land isn't flat, so to build structures you have to level off a piece of land which involves moving dirt from one place to another. After a couple centuries of abandonment natural flooding and erosion will move that dirt around and bury the structures. New settlements come in and build on top of the new surface layer.
For cities like Seattle, the original town was all wood and burned. Prior to that it was prone to flooding. During the reconstruction they decided to haul in dirt to raise the level of the city for better water management, but that would take a while. So businesses were rebuilt in place (but out of brick and stone), while dirt was being hauled in and new street levels were raised. New buildings were then built on top of the existing (essentially turning the existing ones into basements / foundations for the new ones). Similar thing in Chicago -- the city was raised up, and the second floors of buildings became the ground floor, first floor became basements, etc.
