We used the Resource Import tool to bring in the source OS files.
The issue comes into play where the Apply Configuration task kicks off before the Deployment Agent has the chance to install to the SMA. We have circumvented this by applying the join domain configuration items directly into the Sysprep itself... While not my preferred method because the domain creds are present in the file, it did indeed work.
If we would have used SMC to import the source files, would there have been a different outcome?