I have a degree in Archaeology! Grass over time gets higher (takes centuries to become noticeable) Dead grass/ animals/insects/bacteria rot away and become soil which the top layer then continues to grow upon. We're talking about 1500 years or more of deposits in this photo.
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Villa is abandoned -> land sits unclaimed for indeterminate period -> villa becomes overgrown -> farmer claims land, covers what he can see with top soil (at this point the floor is overgrown) -> generations of farming happen -> farm is bought and turned into vineyard -> today
I was in Italy in December and toured the region all around Siena. It was interesting the conversations I had with my guide...today, although we place a lot of value on preserving artifacts like this - in the past, especially in Italy, places and things like this were fairly common. Common enough, to the point that it may not have even been considered special, or noteworthy, 1,000 years ago by whoever may have owned the land.