No they don't.
There's an optimal set of runes for every "class" and "sublass".
It was the same reasoning behind mysteries, that people can customize their champs more but that turned out to be false because there's an optimal build for every "class" and "subclass"
For example, If I'm playing Jhin, what mastery tree do I go down? Do I take fervor of battle, or do I take deathfire's touch? One might say, well it's preference. True it is preference, but that does not make them numerically the same in terms of value. One is clearly better in more situations than the other.
If I'm playing Braum and I have a choice between Strength of the Ages or Bond of Stone, which one do I choose? Well, again, one would say that it is preference. Again, it would be preference, but that doesn't change the fact that Bond of Stone is better in more situations, making it the optimal choice.
It creates a false choice. Do I have a choice? Yup. Does one choice put me at a disadvantage when compared to the other? Yup.
In the case of runes the same applies. What yellow runes should I take on Jhin? Well, I have many options, or do I? Say I take flat HP yellows. My reasoning, well I want more health. Why? So I don't die as fast, of course. But are they best the choice for survivability in lane? No. We know that flat armor yellows are better in providing you that lane safety you're looking for and effectively give you more HP due to how mitigation works. Do I have a choice? Yes. Is one choice better than the other? Yes.
It's a total trap and the only people who fall for it are the newer players.
It's the same for almost every rune type with the exception of very niche cases, like Vlad, for example.
