Quote "prominent placement of “Commercial Themes” link" is actually not really true. In fact, despite the location of the link, it's almost in a blind spot based on how people's eyes view the overall page. When the new theme directory went live, I was wondering where the commercial link was until I took more time to examine the page, only to finally see it come in view. It's located in a darker grey bar and is easily missed.

It appears that wordpress.org is looking to phase out the commercial listings, or at least placing it "all back of the bus".