Human history has typically revolved around either killing people or creatures that are considered to pose a threat to them or avoiding a fight they can't reasonably win. Society "works" because people feel safe that other people around them will not unexpectedly resort to violence for fear of capital punishment or reprisal. If you are predestined to win any physical confrontation there is no reason not to always resort to violence and there is nothing anyone can do to stop you. Unkillable "protagonists" that only "spawn" in a particular group of people, cannot be stopped, trapped, or slowed, only get stronger as they fight, and cannot be negotiated with would definitely pose a threat to everyone else around them. They don't even have to be outright warlike, the "protagonist tribe" can just demand tribute from everyone else using gunboat diplomacy and if they don't comply said tribe will sic their unkillable terminator protagonist on them.
This isn't even X-Men where you have a subgroup of people with supernatural abilities that can occur in any group. This isn't even Attack on Titan, but it is pretty close with a set number of less than ten super-powered individuals tied to a particular ethnic group. However the titan shifters in Attack on Titan aren't as much of a threat because a) they aren't invincible, they can lose fights easily against one of their own or someone using unconventional tactics, b) they can be tricked, trapped, or sealed away, and c) the downsides with titan powers are bad enough that the average member of said ethnic group doesn't want titans running around anyway. Fate manipulation like you're suggesting means they are essentially impossible to fight and there is nothing to stop them from being monsters. Normal heroes usually aren't seen as a threat by the common person because a) they are treated within the narrative and universe as unusually skilled individuals that gained their abilities through hard work, divine intervention, or fate rather than being tied to a particular group b) they are mortal, fallible, and can lose, even Hercules died eventually and Kryptonians always have Kryptonite. They aren't "protagonists" but merely individuals with extraordinary abilities, and aren't at the same level of threat.
That's another big question. Do the "protagonists'" "protagonism" powers work on their own people? Because if that's the case there is nothing to stop them from overthrowing the existing government with physical force and ruling as unkillable god-kings because they can never lose in a physical confrontation. Assassins and underhanded tactics can't even get rid of them. Think having typical Dungeons and Dragons gamer protagonist murderhoboes as autocrats. Bad.
The best way to deal with such a society is to be wherever they aren't. Nomadic tendencies would become common as a way to pick up and leave whenever the "protagonist tribe" are near. The "protagonist tribe" would monopolize the best farming lands and the lands for resources, leaving other peoples with suboptimal places to live because better there than constantly under "protagonist" threat. Any sign of a "protagonist" would be a good reason to pick up and leave, hopefully before they see you.
Advanced technology would be hard to make since nomadic lifestyles don't lend one's self to heavy industry. At best you might get something like some of the northern Asian steppe peoples or some North American Native American groups (flint mines) where there are hidden areas where the protagonists can't get to that make weapons and tools for the rest of the society.
The best way to fight the "protagonist tribe" would be guerilla attacks on non-"protagonist" members. And...and I hate that I'm even saying this...it's highly likely that non-"protagonist" peoples would fight back by trying to genocide all non-"protagonist" members of the "protagonist" tribe. If "protagonists" can't be killed, slowed down, sealed away, or negotiated with, but they are tied to a particular people, then genociding that group of people and making them extinct is one of the few practical solutions people can implement to the problem. However, if "whenever one dies a new one appears fully grown soon after" that probably wouldn't work. But it raises the question as to why your "protagonists" are tied to that group in the first place if they aren't born in it.
Alternatively, if there is any intermarriage between the two groups, the boundaries between them would rapidly become blurred. "Protagonists" would no longer solely arise within the "protagonist tribe", they could pop up anywhere because anyone has ancestry of the "protagonist tribe" within them. It doesn't even matter if there is a particular "protagonism gene" that allows protagonists to be born, because before modern genetics all people will be able to figure out is that protagonists tend to be born in some families more than others. Indeed if your story takes place over thousands of years it is possible that "protagonism" genes could be spread all over the world and their origins lost.
EDIT: The more I think about this the more I think this issue is literally a more extreme version of the metaplot of Attack on Titan,
complete with the breeding issue, ties to a particular ethnic group, other groups without a superpowered bloodline controlling the nine superpowered individuals through propaganda and threats on their (non-super) family's life, dubious methods of inheritance that no one really understands, attempted genocide of the superpowered tribe, and conflict between the superpowered god-kings over control of the non-super members of their tribe (Great Titan War). Look at that for potential avenues of conflict.
The biggest issue is going to be the "protagonists" are always connected to that particular group of humans, which is going to inherently turn the narrative into an "us versus them" story. There's no "convince them to side with you" like Superman or "get protagonists of your own to fight fire with fire". While the Moses situation is possible and it's almost impossible for them to reach the heights of dogmatically xenophobia seen in the Pak Protectors, they have a very strong pressure to always value the lives of their tribe over non-tribe peoples. About the only peaceful solution would be "marrying in" so everyone is tied to the super bloodline.