The heart of your confusion lies in the fact that できる can serve in other roles in which it is not the potential form of する。It's better to think of 出来る as its own completely separate word, which also has a use/meaning that conveniently lets it fill the role of the potential form of する。
Let's look at the definition of できる・出来る in a dictionary (大辞林第2版).
休む is basically intransitive, but it has this transitive usage, too. You can say 会社を休む, 会議を休む, 学校を休む, and so on. Transitivity of most verbs are straightforward, but there are many tricky ones which you simply have to memorize. See this answer for similar examples.
Also note that many intransitive verbs related to movement can take を, in which case を is more ...
It seems that に can also be used for verbs serving as complements of verbs like "order", "promise", "force" also called control verbs in linguistics.
私 は 門 を 開けるよう に 頼まれた
'I was asked to open the gate.'
We need to see the context!
The それら, "those", refers to 『都市伝説』 = これらの都市伝説, "these urban legends".
世に囁かれる and 星の数にも届く are both ...
But my feeling is that it is referring to Kirito as the subject and is saying he "contains" too much airheadedness?
You've got the point. The nuance of 入る here is just like "is contained" or "is inside" as you understand, so that sentence reminds me while he "contains" too much airheadedness, he's not an absolute ...
After some more research, I have come across some interesting explanations. I'll link below the 2 webpages that helped me the most.