"I looked down at the people from on top of the skyscraper [or mountain peak, etc.]"
constitutes acceptable American English usage, but you have to be careful as your other example,
*"I looked down at the people from on the skyscraper"
is not idiomatic.
Perhaps the most common use of "from on" in English is "from on high." To assess the accuracy of this assumption, I ran a Google Ngram here, which shows that published usage of "from on" and "from on high" follow each other quite closely over the past 400 years. I specifically chose the year 1600 as the starting point due to the original publication of the King James Bible in 1611, with many republications of it following rapidly thereafter, (seemingly) peaking in the mid-17th century. These "new" English translations of the Bible, including the "Geneva" Bible of 1560 (among others), greatly influenced usage by countless English speaking writers, including Shakespeare.
Of course there are and have been many other uses of "from on" and "from on high" that have nothing to do with the Bible, including your example of "looking down from on top of a skyscraper," but the parallel "ups and downs" in the Ngram of the two phrases over the last four centuries, for whatever reasons, is still interesting.
Although I am not a Christian, when I was at university 40+ years ago, one of my favorite professors claimed that to be literate in English required at least having read the most important books of the King James Bible and the major plays of Shakespeare. She said that without knowledge of both, a reader will fail to understand thousands of allusions in English literature from the 16th century to the present day.