WebUrbanist explains that the Umeda exit ramp was planned to go through a crucial piece of downtown property, but the owners didn't want to sell:
"Since there was no room to shift the exit ramp, the two sides sat down and began to negotiate and negotiate and negotiate some more. Five years later, the issue was finally resolved though neither side really conceded anything."
Construction happened simultaneously on the building and freeway off-ramp, which technically runs through floors 5 through 7. Lots of pictures over at WebUrbanist.