I always viewed it as just a general acknowledgement of the FF series. He's not supposed to represent anyone, but he is designed to appear like a FF villain.

I still think this is one of the coolest things in SMRPG. I was all giddy when I first fought Cluex because of the FFIV boss battle theme, which is one of my favorite battle music in the whole series. FFIV being my favorite game helped, as well.