Is atheism a scientific perspective?

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See, that is a logical fallacy. That's like saying it's great that my laptop has an internal fan to cool it down, but a designer would have figured out a way to prevent it from getting hot in the first place.

We're not talking about cooling down a component in a computer, I'm talking about a 'design' that has lead to the near-extinction of all life on the planet in the past and threatens to do so again.  The human who designs a microprocessor is limited by his knowledge and resources and the laws of nature.  A God who builds a universe is limited in no such ways.  If his designs are inefficient or dangerous, then they are that way by design.  If my expectations for God are no greater than they are for a human engineer then God either faces the same limitations, is a monumentally inept engineer, or is designing things that way on purpose, which would be terrifying if true.

I think that is another flaw in the argument. It does not necessarily follow that something dangerous or inefficient in a system is the result of a flawed design. It could have degraded to the point where it became dangerous, or some other force could have damaged the system to the point where it is dangerous. For example, we are releasing tons of CO2 into the atmosphere which is leading to warming. The previously non harmful  atmosphere is now potentially harmful. Similarly, an exploding star that releases debris into space may be an instance where the system is running down as opposed to saying that it was intended to lead to problems for our planet. Another example would be the fan example. If the fan stops working, then the laptop could potentially overheat, whcih would make it a threat to the user. It wasn't designed to do that. 

I think you are hinting at a bigger question, though. Why isn't everything in the universe perfect if it were designed by an all-knowing God? I don't know, but I think that perfection is too much for us imperfect people to ask for. If it were perfect, then there would be more room for us imperfect beings to corrupt and ruin it. Would you create an extremely intricate and "perfect" enclosure to house a group of rowdy animals? It would be all the more disappointing for you to see your perfect enclosure be ruined by the inevitable actions of the flawed.