Hi Zachary
The motivation for the changes in theme integrations was to make it easier for most users—for whom the existing workflow was too demanding—not to eliminate the workflow for more advanced users.
So, we will continue to support the Layouts Divi integration plugin so that it can be used as before to design the entire page, including Headers and Footers, although we are unlikely to actively add new features to it.
If you use the integration plugin it should work, and if it doesn't (because of a Divi update, for example) we will fix it.
If you don't use the integration plugin (which is what we now expect of most of our users) then you should find that Layouts and Divi work fine together, but only for the content area of the page.
This approach has evolved over the past few months, and we haven't necessarily communicated that too well. Removing the integration plugin from the downloads page when it was no longer needed was a mistake and sent the wrong signal, for example.
You might like to know that we are working on a new feature that gives back some of the control lost when stopping using the integration plugins. Your Layouts will still only affect the content area of the page, but for each Layout you create you will be able to set theme options from that Layout.
What does that mean? Well, if your theme options let you specify left sidebar, right sidebar, or no sidebar, for example, then a Layout for one post type might specify left sidebar and a Layout for a different post type might specify no sidebar.
For this to work the theme will need to supply a JSON configuration file. It's an opt-in programme that will begin with a handful of themes, but my understanding is that we will provide what is required for it to work with Divi.
With this you may find you can change your workflow to use the odd hook or modification of a child theme to add whatever you want above/below Divi elements from the header or footer – or you can carry on as before.
