I haven't yet played your mod at all - I just downloaded it a few moments ago - but I've been playing around with modding IN, and in particular the tribal countries (well, mostly Byzantium, but the tribal countries too) a lot, and finding through lots of testing and observation how the new rules work for the big tribal governments in the Middle East and central Asia, so I have some ideas on some points in the manual. (I hope this is constructive rather than impudent, as you seem to have done a ton of well-thought out stuff and I'm just picking on one little bit I've been focusing on for the last week.)
The post-collapse Inca rebels built at least one pretty impressive fort, so I don't think you're crazy at all.
In vanilla (though quite likely the many changes you've made have changed this) I found that the arguments for annex=yes were quite different for the "shamanic" vs "animism" pagans. (Not that this has anything to do with the real life meanings of those terms, but it happened that the nations Paradox describes as "shamanic" generally lasted a long time after contact with monotheisms while the nations Paradox describes as "animist" - at least, the Incas and the Mesoamericans - collapsed rather abruptly on contact with Europeans, due more IMO to disease than theology. But the "shamanistic" Iroquois were still a diplomatic partner of the British to 1800, whereas with "annex=yes" in vanilla NA, whichever AI was colonizing North America tended to reach the Mississippi by 1500 in my games. And in Asia the Oirut Horde was just about impossible for the Ming to conquer - the Ming could march their armies around the steppe wherever they wanted as long as they wanted, the Oirut would just graze their horses somewhere else. IMO the Oirut are too easy to conquer even with annex=yes turned off. (An evil modder could simulate that by simply having the Ming map end at the Ming border, and periodically Oirut armies come out of the unknown grassy wastes and start sieging your cities)
I think the Inca collapse is in some ways better represented as the Inca nation breaking, but that's a lot of work to recreate. And of course it's true that noone in Europe was upset because the Spanish had annexed a great kingdom the way they'd have been horrified if 300 people had just grabbed France.
But Mameluks, Golden Horde and Timurids are the three biggest "tribal governments" (although the term is laughable for the Mameluks in particular) and they not only neighbour higher than african tech groups, they're all Muslim tech group themselves, yet they kept their systems of government until they stopped being Mameluks/Golden Horde/Timurids. What you say sounds like an excellent change for the "New World" and African tech group countries rather than tribals per se

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The thing is that Paradox has lumped at least three completely different types of country together in the "tribal" category: Asian horse nomads, the Mameluks, and isolated peoples (whether due to being on the far side of an ocean or being in places where the malaria alone will kill most people from "civilized" countries within a year). These groups don't really have anything in common with each other, and should IMO be separated out.
Well, in vanilla IN there are 4-5 nations that really get affected by these events and modifiers: Timurids, Golden Horde, Mameluks, Incas, and arguably Persians (I don't know about Africa), and only one of these is pagan. I agree that the events are very unrealistic for the Incas, but that's not their point: they're there to keep the Timurids/GH/Mameluks from being superpowers in 1399, and in that respect they're broadly realistic, or at least less unrealistic than not having any such penalties for those countries. Also, in vanilla these modifiers make the Timurids and Golden Horde break up into smaller factions as they historically did (although the time scales are wrong and the successor nations are wrong), and make the Mameluks underperform as they did historically. Now if you've changed things so that "tribal" = "pagan" in your mod, obviously these events/modifiers are going to be completely out of place.
I've been playing around with these events from vanilla IN a lot, and have gotten them to the point where they are actually getting pretty cool - a tribal nation with an excellent chief can grow nicely while tribal nations with poor chiefs fragment, creating nations that would be in the game if you'd started later anyway

. But note that by "tribal nations" I'm talking about the various horse nomads in central Asia - the first change I made to the vanilla vanilla event/modifiers was "not = { tag = INC }"