They don't get them as fast as Europe does, but they certainly can get them.
Most buildings can only be unlocked if you focus very heavily on one or two techs. This requires very unusual specialization to pull off. They also take about a century to research at such a rate, meaning that if you don't follow that very particular strategy you won't get access to them. And that's ignoring that most of these structures were historically just as well know to the Natives as Europeans.
But they can:
(Admittedly it's through a special mechanic, not by the standard merchant-sending mechanism; but they do trade in their own CoTs.)
This is because any state with a CoT will start with a merchant or two in that CoT. As you just said, they have no actual access to the trading system.
Not only can they defeat rebels, they can defeat the French:
And for the record, that French army started out as 22,000 strong when it first landed. Attrition is nasty in the mountains, especially when your Inca opponent keeps scorching the earth ahead of you and recapturing every province you just occupied behind you. Also note that the Inca are still using Native American Spearmen here; they haven't Westernised yet.
Regarding rebels, I can easily say you're ignoring the problem. By loading up an Inca save, I tested my luck against rebels. Using normal battle mechanics it took me 32 battles to destroy a 2 regiment pretender stack. In those battles I lost ~15K men in battle and in 17 of those battles I inflicted no casualties on the rebels. That is not normal.
As for your image of the French, it's clear you used the 10x autowin rule. This is the only mechanic that would allow you to win that battle. If the French had landed 5K soldiers, something entirely within the realm of possibility in EU3, you would have no chance of winning a battle. Using scorched earth mechanics and instantly retaking fortresses is not the same thing as functional combat.
In short, my main problem with your arguments - apart from the occasional attempts to inflate Native American technological achievements far past historical reality - is that you're campaigning to fix a problem that is much less serious than you make it out to be.
In my view you're downplaying legitimate issues because you believe that Natives should be inherently nerfed in numerous ways. I've been arguing that the issues that exist need to be fixed and realistic mechanics put in place to simulate their downfall.
Is playing a Native American nation tough? Hell yes. I'd say the Aztecs and Mayas are pretty much doomed, because they're right in the path of the earliest European explorers. But the Incas and the North American tribes have enough time to research forts and move their sliders to centralised/innovative before the Europeans come calling - which means they have a measurable chance to survive. Probably a much better chance than illapa's 10%, if played by a human against the AI.
It should be tough, but not because you're beaten into the ground by penalties. As I've repeated constantly, being playable and good gameplay are not the same thing. The ability of the player to use gamey mechanics for survival is not an indicator that something is working just fine.
Would more game content for them be fun? Again, yes. But only if it's historical, not exaggerated for the sake of "balance" (or worse, political correctness).
Honestly I find this insulting. You and several others have continually insinuated that anyone who supports the view opposite of yours is a revisionist, an apologist, or is being politically correct. I've not called you Eurocentric or a white supremacist simply because a handful of your points might coincide with those views. Being civil is important. You've provided very little argument that has convinced me and I'm sure you feel somewhat the same. That doesn't mean either of us are arguing for extreme ideas that can be dismissed with a few derogatory labels.