The short answer to your question is “yes”, there are historical and spiritual reasons for most of these rules about feng shui or geomancy. The long answer is that given the long history and sometimes sketchy sources, it is hard to pin down the origins of some of the specific modern beliefs. 

There were many forms of belief about the proper sites for graves and buildings and cities and such. The idea that the dead should face north (and thus the living should face south) is found in the Book of Rites (Brunn p.16), so very early, which is also where you find things about how to site cities.  Guo Pu (275-324 CE) is associated with the Book of Burial. (I say associated with because there was a person of that name, and later copies of the Book of Burial claim to be written by him, but it is not clear that he actually did write the version of it that we have. (Bruun p.22) This is a common problem with a lot of texts.) There certainly are lots of stories from his time about how a grave site could lead to success or failure for descendants. A lot of the early writing on geomancy seems to be about burials, and building temples and palaces rather than ordinary houses. This may be because the literate were more concerned with things like attaining high rank and buildings like that. It was certainly because burial practices were a contentious religious issue. (Ebrey p. 215-219 ) Confucians wanted to eliminate popular practices like not burying your dead for years while looking for a good site, or waiting for an auspicious time. (Something that geomancers could also give you advice on.) People would also re-bury their dead. I don’t have a cite, but there is at least one story about a man being told he would reach high rank but die young if he buried his father in one site, and would live a long life if he chose the second. He chose the first, and once he reached high rank re-buried his father in the second site and lived a long life. Plenty of Confucians condemned this sort of popular belief that people should try to profit from delaying their filial duty to bury the dead. Still, even very “orthodox” figures like Zhu Xi accepted many of the tenants of geomancy (Bruun, 24, Ebrey 218-9)

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Bruun dates “modern” fengshui to the Song dynasty. That is to say, it was in the Song that all of the above was sort of systematized into the Hongfan Five Phases (Fujian) school and the Orthodox Five Phases (Jiangxi) school, although he also cautions that many texts and practitioners will draw from several traditions without worrying about it too much. (Bruun 27-29) This is also about the time the “modern” fengshui compass seems to have emerged.

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 With relation to buildings (which is what you asked about 😊) all of these schools have to do with how to site buildings and villages and graves in proper harmony with the flow of qi (breath or breath of nature Bruun, 108 ) and the five elements and yin and yang so as to bring all sorts of benefits to the family, including prosperity, happiness, long life, and procreation. (Bruun, 59) To some extent you do this by putting things in the right place, but you can also encourage or retard the flow of the elements by positioning things near mountains or water or building walls or whatever. Some of these rules have the practical effect of protecting the village (or house) from floods or typhoons or wasting arable land. (Fan Wei, p.42) 

Bruun and the various works of Ronald Knapp are probably your best guides to how this works in practice. Bruun is particularly good on modern aspects of fengshui

Sources 

Ole Bruun An Introduction to Feng Shui Cambridge University Press 2008

Patricia Ebrey “The Response of the Sung State to Popular Funeral Practices” in Ebrey, Patricia Buckley, and Peter N. Gregory eds Religion and Society in T’ang and Sung China. University of Hawaii Press, 1993.

Fan Wei “Village Fengshui Principles” in Ronald G. Knapp ed. Chinese Landscape: The Village as Place University of Hawaii Press, 1992

Knapp, Ronald G. China’s Traditional Rural Architecture: A Cultural Geography of the Common House. Honolulu, Hawaii: University of Hawaii Press, 1986. 

Zhang Juwen. A Translation of the Ancient Chinese the Book of Burial zang Shu by Guo Pu 276-324. Lewiston: Edwin Mellen Pr, 2004.