Good to hear, really look forward to this converter having all those options!No tribes currently convert as nomads, however, I plan to eventually have it so that there will be 3 options for nomad conversion: No nomad conversion, nomad conversion based on government, and nomad conversion based on both culture and government. The no nomad option would convert migratory tribes as tribes like they are currently, the government option would convert all migratory tribes as nomads, and the culture and government option would convert migratory tribes as nomads if they have a steppe-based culture, such as Scythian and Hunnic.
There is indeed a way to change them, however, doing so will require going into the province history files and changing each province effected. It will be fixed at some point, but other things such as improving the way Christianity converts from the Timeline Extension mod have to take priority first
Another thing though, when I convert a save that's using Invictus, the flags for every country seem weird and not the same ones as when a vanilla save is converted, this normal or a bug?