The Qunari "came down to the south" according to bull and they look nothing like Qunari according to Bull. We don't know if this is something Bull is told or something that is true.
If the Kossith are not the scaled ones I think they (the kossith) are whatever the Qunari are supposed to be, the Qunari are described as a mistake by Cory and that "their blood doesn't belong to them" by Kieran and that he's sorry for what happened to them. Which lends credence to the idea that the Qunari are a failed experiment. I think the Kossith wanted rid of the failures that the Qunari are and so the Qunari had to go south to escape the Kossith.
On the other hand I think the Kossith could also be a by product of the scaled ones. Reptile people would be closely related to dragons, Qunari are very dragon like (with elf features) and perhaps some Tevinter Magister thought it would be a fantastic idea to breed the scaled ones and elves to create the Qunari. The successfull creations were the Kossith, the failures were the Qunari. Both escaped and went north, then as I said above the Kossith for whatever reason started to push the Qunari out and possibly went to war.
*shrugs* but that would be crazy.
[edit] to answer your question Maybe. We might have seen a Kossith I think. Koslun (the guy who created the Qun) was a Kossith.