Is atheism a scientific perspective?

[The Grand Nudger]

Well for one, time limits it.

Sure, and?

We don't know how many replication events there have been, but as we continue to unveil new layers of complexity, we should be less confident that there have been enough.

Enough what, enough time?  Billions of years multiplied by many more billions of living subjects seems like it crosses the threshold for "enough" handily.  In any case, if it's "too complex" perhaps that';s just a problem of perspective on your part. All of life shares a great deal, either that shared heritage is too useful, too entrenched, or there hasn't been enough time to significantly diverge. Maybe it's "too simple"?

Also, I think the mechanism is inherently unlikely to produce new information.

Ah, but no one cares what you think about "new information", since you're categorically wrong from the very bottom of this dumpster term to the top. Call it old information, if you like, or repurposed information, ultimately, the terms you use to cloud your uninformed doubts do not change the process or it's outcome.

Changing sequence doesn't add nucleotides to the system. The only way to do that is to have a duplication event or a retrotransposon replication and reentry event. From there, the sequences must mutate slightly. If they mutate too much, then they will lose function (at least this is what is virtually always observed). That, coupled with the fact that mutation frequency is so low seems to make the whole mechanism questionable.

Questionable how?  You yourself have just noted that we observe mutation.  Mutations have been occuring for billions of years, in every individual example of life, the cumulative effect of all that change isn;t exactly going to be negligible, now is it? Vestigial organs and structures exist, sometimes...function is lost, and it doesn't actually take a mutation for that to happen. I find myself asking again, what's the problem?