You are correct that you can also build a custom nav using that WordPress feature. We have a good article about that here.
The WordPress plugin is used often by people with less technical knowledge of customization within WordPress, although many Designers use it to give their clients a way to easily update and manage those page links from within the Plugin Admin page.
The main feature of the Plugin is the ability to pull Custom Links into your WordPress site, without having to copy and paste the links from our Control Panel. Those custom links are very helpful to gaining traction with search engines, and getting pages indexed.
We recommend that users select a custom subdomain such as www2.mysite.com or homes.mysite.com for the IDX pages. Here's a good article that describes how to do that.
If you decide to go with www. as your custom subdomain, be sure NOT to select www. or non-www. in your Google Webmaster tools control panel. In other words DO NOT choose a preferred URL there if you choose www. as your subdomain. Also, don't choose www. if you already have a lot of current pages indexed there. Go with www2. instead. Check that by typing "site:www.mysite.com" into Google search.