In the sentence, "When one considers the many ways by which organisms are completely destroyed after death, it is remarkable that fossils are as common as they are.", what is referred to by the word "they"? Moreover, is it possible to compare a subject with itself? For example, "The stars are as bright as they (the stars) are. Thank you!
It's a fairly standard reflexive comparison, comparing assumption with reality. Another example:
Given that the common housecat's insatiable curiosity frequently gets them into potentially lethal situations, you have to wonder why the trait is as ubiquitous as it is, or how cats are as numerous as they are. Thus the idiom that a cat has "nine lives".
In this sentence, the assumption is that cats should be either less curious or less common, compared with the reality that cats are both very curious and very common. Your example sentence states a similar argument. Given (some condition) we would assume fossils should be uncommon; nevertheless, the reality is that they are very common.
However you would normally use this expression when you have first given some reason to believe there is something unusual about observed fact. "The stars are as bright as they are" means nothing without some explanation why they should be less bright.
Given all of the matter that should exist in the universe, it's odd that the stars are as bright as they are, as their light should be at least somewhat occluded by intervening clouds of diffuse atoms. We have to conclude therefore that all this matter is somehow invisible or at least completely transparent.
(I'm not a physicist and so this example is completely made-up, and is probably a terrible explanation for so-called "dark matter" -- which nevertheless should not be as "dark" as it is)
[Edit} As Accumulation points out, you can also use this expression when refuting or dismissing some potential objection:
Although the opposition might whine and moan, there is no reason to be surprised that taxes are as high as they are when we are essentially at war.
The speaker in this sentence offers a counter-argument to the opposition's unspoken assumption that taxes should be lower.
There may be other cases where you can use this structure, but most will rely on the same disparity between assumption and (perceived) reality