The attribution to Fu Xi places the arrangement at the mythic beginning of Chinese civilisation, and that placement is itself a claim about authority rather than a historical record. What can be traced is the diagram, and the diagram is medieval. Circular and square charts of the trigrams and hexagrams became prominent in Song dynasty scholarship, associated particularly with one eleventh century thinker who built an elaborate numerological cosmology around them. Their establishment as standard came through the commentary tradition.
When the dominant Song synthesis of the classics incorporated the diagrams into the authoritative reading of the book of changes, they were printed at the front of editions and became for later readers a part of the classic rather than an addition to it. Most people meeting the arrangement today meet it in that position. Its practical use follows from what it depicts. Because it shows the trigrams in balance and not in motion, it is used for contemplation, for the theory of how the changes work, and in internal alchemy, where the pairing of opposites is the operative idea. Siting and directional practice use the other arrangement, and confusing the two produces a system that does not work on its own terms.