Am I misunderstanding the purpose of Microsoft Deployment Toolkit and WDS?

Before you capture your WIM, configure your reference computer with whatever applications you want to have pre-installed. When the WIM is applied to a target, all that is left to do is join it to the domain and apply any updates.

With that said, the beauty of using MDT (and by extension, SCCM) is that you can create separate application packages that can be updated independently of the OS. Adding/removing/updating applications doesn't require a new image build every time. In exchange, you increase the time it takes to deploy an image to a target.

For us, the ability to keep applications separate from the OS image has made management of applications and images MUCH easier, but if you're in a situation where you have identical configurations for ALL machines and only do image rebuilds on an infrequent basis, then rolling it all together would be a better option for you.

WDS provides PXE boot capacity and the the ability to capture and deploy images. MDT provides a ready way to inject drivers and execute scripted installation steps. You can use a captured WIM created by WDS in MDT - I have done so on a few occasions.

My personal preference is to totally avoid using captured WIM images. While they work I have found the process to be more trouble than it is worth - fighting with chronically outdated images is a royal pain in the butt.

To integrate the two use the boot WIM image created by MDT as a boot option on your WDS server. You can use the WIM created by the capture process at that point as part of a scripted install.

I personally do the OS deploy with a stock WIM image, inject the drivers and make any other customizations (such as making a copy of the install image on the local drive) via MDT and deploy the software stack via EminentWare.