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I think you are losing perspective. Here's why.
The fundamental reason that blogs have gained a reputation for having an SE edge over other types of sites, is that genuine blogs tend to become much larger collections of text-based content, than other site formats.
In addition to scoring well for content volume, it is also natural for many blogs to evolve around a topic, albeit sometimes broad in scope. Thus without conscious effort on the part of the operators, they inevitably become rich in relevant keywords and phrases.
If the key factors are indeed content volume and site depth, then almost by definition, the impact of a single article on the SE score for a site is minimal. That is true both of its positive impact as well as any negative impact from considerations such as you mentioned.
Which is not to say that you cannot avoid those negatives, while at the same time reinforcing the positives: take a look at alistapart.com as an excellent example. Articles do not themselves appear on its main pages at all, instead you get a summary of what an article is about. Then you get the article itself. And on other pages you get article titles and/or brief excerpts.
This approach not only avoids duplication, but provides the opportunity for articles to be written naturally (making them generally better for their readers). They will include a random, although relevant collection of keywords and phrases and - although I doubt Jeffrey Zeldman bothers - a tighter keyword focus could be provided in the summaries. Probably the main advantage generally is that the summaries swell the content still further.
SEO nirvana is if your site is recognized as an authoritative source. There are many elements involved in that and only a relatively small number of sites achieve such status. But any movement you can make in that direction is a good thing and the key is not to try to fake the search engines out, but to actually try to make your site an authority on its topic from its visitors' perspective.
I don't pretend that a half-assed site cannot bump its SE score by using tricks. But unless the operator knows exactly what he or she is doing, such tricks are as likely to backfire as help. And if they work, we are still only talking about raising a poor or mediochre score a couple of points. For most people, it would be more certain and take no longer, to write two "natural" articles, than to labor over the SEO appeal of one. And your visitors, who after all are the people from whom you actually earn money, in most cases will respond better too.
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