What do you mean by "all Amazon was saying"? That's the crux of the issue: whether publishers will allow themselves to be told by Amazon that they cannot sell over a certain price in their market, or whether they will be allowed to sell at whatever prices they choose.
It's a fundamental question about how the online book market, so dominated by Amazon, will work.
Your second paragraph doesn't have a clear question; what exactly do you want to understand? I'll try anyway:
The marginal cost of producing eBooks doesn't really effect the price-fixing problem. The OP's point is that publishers need the flexibility to try out pricing schemes on the Amazon marketplace to discover what works, but Amazon won't let them. Ultimately, he claims, this will lead to worse results for the consumer because Amazon will be an inefficient marketplace due to the inability of the publishers to recoup costs on books with high initial prices which they can then follow with low prices later.