This is because His rising over the Throne after creating the heavens and the earth in six days is known through the revelation brought by the messengers, as Allah has related in the Quran and the Torah.
As for His being above His creatures and separate from them, this is known necessarily through the innate disposition shared by all the children of Adam. The better a person knows Allah, the more devotedly he worships Him, the more frequently he calls upon Him, and the more his heart remembers Him, the stronger and more complete his necessary knowledge of this becomes.
Thus, the innate disposition is perfected by its revealed counterpart: the innate disposition makes the matter known in general terms, while the revealed law explains and clarifies its details and attests to what the innate disposition cannot establish on its own. Such is the matter. And Allah knows best.