I assume it was a nod to the Lex clone story in the Superman comics. It all has to do with Rosey not wanting to return originally. This is all Brian and Kelly's fault really, since they went ahead and still did the Luthor survived story line, hoping to eventually convince Rosey to come back, they introduced that story line in season eight and had us all teased only to reveal that it was some generic stunt guy (no offense to him) as Lex with some voice box. Remember how pissed off most of us were during that story arc that they went ahead with that story line without Rosey?
Again...the Clone Lex IS Lex Luthor. He possesses all the memories of the original (except for the ones that Tess wiped out of his time in Smallville and knowing Clark's secret) and it's important to note that the clone himself acknowledges himself as Lex Luthor and doesn't have a problem being a clone. Just as the comic book clone did, until that was retconned out I believe. LOL. Make no mistake...the clone is Lex.