I'm going to break this up for you into a few sections because you're raising a few points.
Open Source deliverable CMS packages like Wordpress, Drupal, Joomla, etc, cover a lot of use cases, but the nature of their deployment is that the content management portion is usually one sliver of the functions and/or portals it has to serve. I think maybe you haven't been exposed to these sorts of environments, where Wordpress will be the blog engine and Magento will be handling the eCommerce, and there's a custom built product in between that marries all of the processes together.
That being said, there's a TON of built-from-scratch work, especially for these types of situations. Open Source (or paid software for that matter) very rarely satisfies the needs of every company ever, especially when you talk about manufacturing-based businesses and similar industries. I find that out-of-the-box work on the popular packages is very common, but I think a good programmer or team uses the engine and really delivers something that meets the business needs, not adapting the business needs for the software. There's a very big difference between the two.
Design patterns are really important, there's no denying that - but I think the introduction of MVC based frameworks has really morphed the thinking of PHP development. If you'd really like to continue educating yourself as a programmer, I highly suggest getting in-depth with an MVC framework and building some stuff from scratch.
Also, regarding WordPress plugins - that can potentially be development hell. WordPress' architecture, in my opinion, is really starting to show its age. I hope there's some thought being put into its future, but I'd stay sharp on pretty much everything else either way.