This came up on my social radar robots recently and it is quite an interesting read. I am a thesis.com customer so this is all news to me. Remember Thesis back in the day? That was a wordpress theme that had such huge commission for affiliates that pretty much everyone was using it. It did over time get caught with by Wordpress out the box core functionality but things like having CSS styles that would overwrite default values and remain in tact after theme updates were very good in their day.
Personally I always had a problem with having to learn another set of rules to layer on top of Wordpres to get it to work, but these were the early days of the web.