Okay I got two answers here. Sorry it's long.
The system determines the class based on your potential (aka what you are good at). If the awakening happens when you are working on that potential you get a higher class compared to having one for survival, which is why they were so many F rankers when they were having everyone pass through a near death experience and not something related to their rank.
The s rankers are also determined the way (some were athletes before awakening).
But there is also the thing of some stronger S rankers like the ML brother and the dragon sister, that I suspect they were placed in the world before the dungeons to kind of "prepare" better. And the parents left cause they knew something was off about the child.
About the ML being a custodian, he literally got that cause ge had custody over his brother before the dungeons and the brother turned out to be an S class, wouldn't be a custodian if the brother got any less of a rank like 'A' class.
And that's where the getting rid comes from, if he is the custodian he would have some level of influence on the one he cares for (like parents). And parents often times influence which way you go, but are also your weakness, even more so in a dangerous setting.
So they took away that influence to better control the S rank and removed the one weakness.
This time they just noticed that by removing the weakness, like how the bad guys tried before the reversal, they end up losing the S rank. So decided to reevaluate
And about Peep, I am completely sure it is the white bird of time the others are looking for and that it is so small because it actually took care to preserve and safeguard the brother's body since it is aware of the future. I am just so sure of that theory and will be shocked if it's not
Idk if my question will get an answer or not later, but how did the system decide what rank to give to a person. Like yeah I like how they say 'don't limit yourself just for being an F-rank' but I'm still questioning what's the deciding factor for each person rank. I know it'll get an answer in the future but my other question is why did the 'systems' kill off people that have custodian skill in others world. I think it also relate to how 'I love you' is the keyword to take in any ranker. Maybe in previous world people that have custodian skills gone on rampage and abuse their power ig. Previously I have a question about what's the deal with the white bird in Yoojin custody but unfortunately I got flash by a spoiler a little bit. But my theory is I thought that Peep is actually Yoohyun that died before the reset but I'm not sure anymore.
But the sad thing is we probably need to wait more than 5 years till the manhwa completed. Like it literally have 800+ chapters (not including side stories and sequels), like holy shit by estimation maybe this manhwa will have 500+ or 600+ chapters? Idk I'm avoiding the novel as much as I can to avoid spoiler, so idk how many chapters per novel for 1 chapters per manhwa. Well I'll come back to this manhwa maybe next 2 or 3 years for sure