It makes me wonder if the companies behind that online game and auction site were "sold" Wordpress by a developer/designer as a way they could easily update their website. Perhaps whoever pitched Wordpress as a solution in those cases didn't have the knowledge to build a fully functional website from the ground up without Wordpress.
As a fellow PHP developer, I can say I share the heart sinking feeling when I see "functions.php".
A lot of it is due to the fact that it's much easier to sell an end-user on a plugin to their existing site that requires little to no server configuration than a completely separate system.
Whether or not it makes sense as a WordPress add-on is not really taken into account by users, who just see it as easy to set up and manageable from the same dashboard as the rest of their site.
Perhaps they were comfortable with WP, perhaps they didn't want to spend time reinventing the wheel, perhaps they didn't want to have to support a massive body of code.
As a fellow PHP developer, I can say I share the heart sinking feeling when I see "functions.php".