Your thoughts do make sense.
From the article - Yes, the paid inclusion program gets the spider to visit your site sooner, but just having spiders visit your site won't get you rankings. Your site still needs to be full of relevant content, themed correctly, have no major server or spiderability issues and be void of any deceptive practices.
Paid inclusion is about spidering, and the converse of the above applies as well that a site that is relevant and full of content, themed, etc will rank with or without paid inclusion. My theory, and it's a tough one to verify, is there is a key difference with paid inclusion vs non paid inclusion. I believe when paid inclusion is utilized Yahoo has a review process (think human at computer). imo, that review stage initiated by paid inclusion 'might' carry weight within the algorithm/organic results.
A couple thoughts ... I do not disagree with the 'real estate' counter arguement IF it is providing the ROI 'and' that budget could not be utilized better by targeting other keywords, etc. At the same time, keeping the competition out of the space can be essential - but I agree an organic ranking would likely occur.
Only way to know for sure, is to track, test, track, test, test, test. If other keywords are a consideration with this campaign - I would imagine an account manager could assist you with including some negative keywords/brand in your campaign. But of course you don't want to exclude your site from the index/serp.
My approach would be to shift that budget to other more productive/roi keyword areas. Most who search your brand will find you, regardless of pfi/ppc