I have seen it argued that in many areas this was, without anyone explicitly realizing it, an evolved (historically, not biologically) response to mosquito-spread illnesses. In short: people saw, over many years, that living in marshy, brackish, wet, low-lying areas tended to result in lots of nasty illnesses. From this many incorrect ideas about illness came from, including the famous idea that it came from bad air and dampness. We now know that some of these illnesses actually were spread by mosquitos, notably but not limited to malaria. In areas that had pathogens of this sort, which included a lot more locations than most people realize (e.g., parts of England), people who lived in higher, well-ventilated housing seemed to do better on the whole. This is because mosquitos apparently have a harder time reaching such areas and staying there. This is discussed at length in Charles Mann's 1493, in chapter 3 ("Evil Air").

This approach to understanding historical trends strikes me as plausible but a little underwhelming by itself. How common is the sentiment of a house on the hill, historically? Do you find it in non-malaria (or yellow fever, or whatever) zones? How do biological activities resonate with cultural ones that might already exist? Are there other factors involved? Why do they persist over time? Is the "rich people like manors of this sort because of an unrealized response to malaria" story just a "just-so" story? I don't know. I feel like it has the trappings of all that. I'm not saying this might not have played a role; I'm just saying that it feels insufficient as an explanation. And I actively distrust the part of my brain that says, "ah, that's a satisfying, science-like answer to a why-is-culture-the-way-it-is question! I would like to believe that!" And to be fair, even Mann points out there are large interpretive leaps involved.