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To ensure this, we have placed the directory with the dynamic ColdFusion pages in a specific directory, which we have identified through robots.txt as "do not index." We're assuming that Google respects our wishes.
The debate is over the impact on PR. Suppose page X has four links out, one of which is a dynamic URL that goes to this forbidden subdirectory. There are thus only three links to indexable pages. Is the PR of page X distributed to these three as though there were only three links on the page, i.e. 1/3 to each? Or does Google downgrade them because there are four links physically on the page, and thus distributes only 1/4 to each of the three, with the 1/4 that might have gone to the forbidden URL instead just vanishing?
If this is true, then a large site with a lot of affiliate links on each page, even if they pass them through a script in a do-not-index subdirectory, is going to suffer a huge PR loss. It means that the "oh, why not," kind of minimal affiliate deals probably cost more than they bring in.
So I agree that the pages will get their share of the PR.
However, the impact of that might not be as great as you think - firstly, Google estimates the PR of a lot of pages and secondly, the PR "bleed" will be so minimal as to make no difference at all.
So if you have 30 internal links and 3 external (affiliate or not), you still end up with 90% of the PR getting recycled back through your own pages.