I wouldn't think that Gat is a clone of either the Zinyak or Saints because...
1. The timeline doesn't fit. Gat 'died' in the beginning of Saints 3, which is over five years before the Zin even set their sights on Earth, as far as we know. Even if they did have the opportunity to clone Gat, why would they? They have no way of knowing that the Saints would later rise up to become the leaders of the free world, and thus become their primary target.
2. You can't clone anything without genetic material. It's possible that the Saints got Johnny's genetic material from the guy in TwC, but if they were able to clone Gat for 5 years+, why didn't they before then? Why is the Boss surprised to see Gat, he would have known Gat was a clone and thus would not have greeted Gat as though he was gone for a while. If the Zin cloned Gat, then how did they acquire the genetic material? Presumably they didn't know about the kid from TwC, and Gat's body was never found, unless you count Zombie Gat which, I'm not sure you can count that.
3. We don't even know if the Zin have access to cloning technology. Sure, a lot of their race look the same, but that's more a limitation of the game than anything. There could be other permutations of the race we don't know about, as well.
I'm maintaining that it's the original Gat, myself. How he came to be in the possession of the Zin, however, I have no idea.