This is an open question because maybe I'm missing something, but it's always strange to me when they're called 'overpowered because they're accessible day 1' or 'free bonuses' when they aren't..?
Unless you skip day's or otherwise cheat to get them all immediately (which im not saying is a bad thing mind you, play how you want) You have to survive and play the game to earn the points, they aren't immediate upgrades and I believe they are/should be balanced around that fact. Like, surviving as long as you can is, for a new players especially, a big intrinsic goal of the game.
So, skill points are a reward given to the player for being good at the game, one that sticks between worlds and the world wipes that result from death. Beyond being a way for new players to measure their progress and a carrot dangled to start another world and try to push a little further into the year, they open up new options, obviously, options made more meaningful due to their persistence between worlds and servers.
Additionally, it gives players a motivation to try new characters, to go through and unlock all of their skills to, something thats, well, really fun!
And so, the alignment perks are the ultimate reward for 'mastery' over the game, you beat the big bad boss, prove you know what your doing and can deal with what the game throws at you, and you get something big flashy and cool! (Unless your wolfgang) These perks should be powerful, they should make surviving through the early game easier, they should be relevant during rifts, because to access them you had to have already "beat" one of dsts hardest challenges.
Well, unless you skip days, but skipping days or beating the bossess in god mode genuinely should not be taken into consideration for skill tree balance and analysis. If your playing the game unmodified, you do have to earn those points by playing the game, and beating the games hardest bosses and their associated questlines.
In a way they are the dst equivalent to ds chatacter unlocking, in that they are a meta progression aspect in a game that, I promise, is still permadeath on default settings. If anything it suits dst's multiplayer nature very well imo, sense these milestones carry over between servers, so even if your hopping between public servers, you are meaningfully making progress.
Is it perfect? No, and there's plenty you can criticize about it, but I do genuinely think its a good addition to the game and adds significantly more then it subtracts.
Its more then "reworks two" it's the implementation of meta progression, and I don't think many people see it that way, and i really dont understand why?
But again, maybe Im missing something and Id love to hear other peoples two cents, this is just my opinion after all.