What if religious claims about the real world were correct? Well, let's take the Bible as an example. It says a lot of things that those who wrote it could not know from their own direct experience, and it is claimed that their source was direct inspiration or information from God.
If that were true, the facts of the world would gibe with the story. Since the authors of The Book couldn't have known this in any other way, it would reinforce their claim of divine inspiration. Science would have to accommodate. The correspondence of facts to the Story would lead us to believe the source were true, and we'd have to fit our understanding of the material world to the explanations. Like the age of the earth.
In fact Darwin worried about his version of the young earth--not Bishop Usher's estimated 6000 years, but physicists' and astronomers' estimates of how long an earth-sized molten rock would take to cool down to its currently observed temperature. That might be millions, or even a couple of hundred million. But was it enough for evolution to have happened as Darwin thought it had?
How old is old enough?
This is a question that reveals much about the nature of science. If we were to accept a Biblical explanation, the age is what we're told it was in Genesis. We would have to fit every other explanation to that assumed truth. The key word is assumed. Science is empirical, but it is also theoretical because we try to generalize from what we've seen to what we haven't yet seen. We build an axiomatic system in which we take some things as true and use them to explain real world data. Where things don't fit, we either must abandon or modify our axioms, or develop better explanations that are consistent with them.
So, if we accept 'evolution' as true--that is, that life today is the result of a history of descent from common ancestry, then we have to fit the facts to that assumption. What that means is that, however old the earth is, it is old enough! The 'how-old is old enough' question is really not a scientific question.
We simply must fit our theoretical understanding of life's diversity, the fossils, radioactive dating, geology, mutation rates and comparative genome structure and variation to our assumption that evolution is a fact. The success of this integration is overwhelmingly in favor of that assumption. But where current ideas are wrong, where things don't seem quite to fit, we simply have to question whether we've really understood our data or measured it accurately, or hunt for some missing or errant aspect of our theory.
If evolution happened, then -- it happened! Our job is not to ask if it could have happened if we assume it happened. It's to understand how it happened.
Sadly, the facts of the world don't fit with Biblical explanations. That's the reason, and not atheistic hostility to believers, that science does not accept the truth of literal Biblical explanations. It is why some scientists would say rather uncharitably that it is ridiculous to cling to such explanations anyway. It's why such persistent beliefs in religious dogma are often sneeringly likened to beliefs in the Loch Ness monster or Santa Claus.
And that's why the question whether complex traits could have evolved without an Intelligent Designer is not a scientific question. If evolution happened, then it must have happened somehow and we have to figure out how. If we have things we can't easily explain, well, that just means we have work to do.
The history of human knowledge shows clearly that things that seemed obvious may turn out to be wrong. Revolutions in scientific thinking do occur, and the discovery of evolution was one of them. But there is nothing in prospect that suggests that evolution itself is on shaky grounds.
Our inability today to explain everything we observe suggests that there could be some phenomenon we've not discovered, or principles we've misunderstood. But a lack of completeness in our understanding is not in itself an argument for some specific alternative explanation such as a Biblical one -- or that humans evolved from aquatic apes. It doesn't justify funding research to prove those claims as plausible alternative hypotheses, because they have already been found wanting. For example, the earth itself tells us that it is not just 6000 years old.
But if there is nothing to shake our assumption that evolution happened, the great amount that we don't yet understand should shake any complacency that we already know it all and should warn us not to become as dogmatic as science's critics are.