As an adverb “even” has the following meanings.
1. To a higher degree or extent; yet; still. Used as an intensive: “an even worse condition.”
2. At the same time as; just: “Even as we watched, the building collapsed.”
3. In spite of; nevertheless; notwithstanding: “Even with his head start, I soon overtook him.”
4. Indeed; in fact; moreover. Used as an intensive: unhappy, even weeping.
5. To a degree that extends to: “loyal even unto death.”
You do not have to think of “even if” as one unit. For example:
In the sentence, “Even if I were to go, I would be late,’’ the word “even” serves to intensify the following subjunctive clause introduced by “if” which here means “in the event that.”
“Even if that’s true, what should we do?” “Even” is an intensive and “íf” means “granting that.”
In your example, “Even in the darkest ages humanity has endured,” the word “even” still functions as an intensive. You are using “even” to emphasize that humanity has endured.
Your second example is incorrect. The reader would get the feeling that “even” is an intensive and “if” means “granting that” and introduces a subjunctive clause. The reader would expect something to follow. For example, one might say: “Even if in the darkest ages humanity has endured, that still does not attest to any nobility in man.”