Superman follows the vanished into the Phantom Zone and meets Clark Kent.  We now begin to understand that Superman created a world within the PZ—and idealistic alternate reality—in which there was a Garden of Eden.  But the “Clark” that is here isn’t loved by the “real” Lois Lane who has now joined him.  She loves the “real” Clark Kent–from her own reality.  Or does Clark’s statement mean that she loves Superman and not Clark, that she loves the God and not the man?
This thread isn’t explored any further, really, which is too bad, but you can’t blame Brian Azzarello for that.  This storyline was so rich, and had so many opportunities for deep character development, that we can let this little comment slide.  I assume that if Azzarrello had stayed with the title after this storyline, he would have delved into this further.