There are two ways a Wordpress site can be built, and I am always surprised that many people do not know this. In fact, some people ask why they should even care… As long as they get a site they are happy with, that is all that matters right?

This is a big topic that could easily be covered in more depth and detail, but my answer is below, in a way that is hopefully straightforward and easy to understand.

1) Prebuilt WordPress: 
-  Rather than hand coding, off-the-shelf Wordpress themes and plugins are installed and configured.
-  The No Code Revolution is here!

2) Custom WordPress: 
-  Using the basic coding and infrastructure of WordPress, custom themes and plugins are built, as per a project’s specific requirements.
-  Real sites need real development!

So why should this matter?

Site Maintenance
-  Each site feature usually requires its own plug-in. 
-  To allow for a one-size-fits-all solution with many optional features, prebuilt sites are often created with many plug-ins.
-  Custom sites only have the plug-ins necessary for the particular project’s requirements.
-  Plugins need to be updated regularly—the more plugins, the more time required to keep the site up-to-date.
-  Myth: Site maintenance is just a matter of hitting the "update" button. This is often the best way to break your site!
-  Custom sites require less maintenance.

Site Security
-  Since the code of a ready-made theme is available to anyone, there is always a possibility of the website getting hacked.
-  Also, the majority of ready-made themes do not provide security updates on time. And when they do, these updates may not be done right away, especially when there are lots and lots of plugins that need constant updating. This leaves a loophole when certain plugins may not be up-to-date, leading to the site getting hacked.
-  Custom sites, built with custom code, can avoid these security loopholes. The code is also not available to all the users, making it tough for the hackers.
-  Custom sites are more secure.

Site Flexibility
-  A prebuilt site may require complex features or template types that are tricky (or even impossible) to addressed down the road within the confines of its “canned” theme. If you decide you want to add a new feature or template type to a custom site later, you don’t have to worry about being restricted by a template theme. 
-  As the site grows and develops with time, these changes can be made to improve user experience more easily with custom themes.
-  Custom sites form a stronger foundation for the future.

Site Support
-  Though the owners of some pre-built themes do go above and beyond to provide support, most is very limited, if there at all. The support that is there is often mostly in terms of functionality, not design.
-  Myth: All coding is done exactly the same way, so it is easy for one developer to work on another’s code. To do this, the logic behind the code (eg: a pre-built theme or plugin) must be understood. This is not easy, as the logic can be really different from one developer to another. In fact, sometimes it can take much longer to fix a pre-made plug-in, than just coding the feature custom in the first place.
-  Custom sites make support easier.

RIO
-  Custom templates are built with particular goals and objectives in mind.
-  Prebuilt templates don't know a business or its audience.
-  If the prebuilt route is taken, you may end up with a site that doesn’t have a great RIO, rather a site that is:

Actually pretty expensive
Bogged down with unnecessary plugins
Vulnerable to attack
Not very customisable
Not very easy to fix

Full confession: MOTHandRUST typically choses to build custom WordPress, though of course there are always exceptions. I do hope this article sheds a light on why, and also why you should know how your Wordpress site is built.