I'm hesitant to even post my opinions as at least two highly respectable, and respected, academics have already posted their views from the inside of that process. Each has expressed different views and each one is accurate.
I guess therein lies the flaws and the benefits of peer review? It's a human construct and prone to subjective biases. The thing is, how could the peer review system be improved? Or more critically, for those who have distrust or contempt for the process, what could replace it that would be an improvement? Tough call, huh?
Someone who Byrd might know in a professional capacity is the archaeologist Dr Michael E Smith. I've been reading his blog (Publishing Archaeology) for a long time now. He's described some of the issues surrounding peer review in articles like Rejected by Science!
It was one of his subsequent postings that has stayed in my mind and features a pretty decent quote that relates to the value of peer review.
“Inquiry of a scientific mature, I stipulate, aims to be cumulative, evidence-based (empirical), falsifiable, generalizing, nonsubjective, replicable, rigorous, skeptical, systematic, transparent, and grounded in rational argument. There are differences of opinion over whether, or to what extent, science lives up to these high ideals. Even so, these are the ideals to which natural and social scientists generally aspire, and they help to define the enterprise in a general way and to demarcate it from other realms.” (Gerring 2012:11).Science Type 1 versus Science Type 2
I think that these views really express the spirit of peer review even though it might sometimes fall short.
In your examples of purported failures of peer review, my eye was caught by the Virginia Steen-McIntyre reference. That's a can of worms! It remains way more complex than a simple refusal of science and archaeology to accept extraordinary evidence of the early population of the Americas. I know Byrd is intimately familiar with this subject and will be far more insightful than I can be. Nevertheless, it's still part of an ongoing process of peer review with new evidence constantly being examined. A large problem is that a population of humans can't just be said to have existed ~250ky before accepted populations had even arrived in the Americas.
It's a popular topic in conspiracy culture, but I've yet to see any conspiracy theorists actually discussing the nitty gritty of conclusively dating diatoms at the site. There's been a long-standing discussion at Hall of Maat about problems surrounding the dating of the site. If you use their search engine and look for 'Sam VanLandingham,' you'll see what I mean.