Taylor, who heroically answered my support ticket at 11:20PM on a Friday had this to say:
"Anything you need to store in storage I would put in the "storage/app" directory. That is the folder structure that Laravel ships with out of the box and is generated by Envoyer. Any other custom folders in the storage directory above that will need to be created manually on the server."
In my "special" case, I had to move the folder containing my reference data to the project root. The reason is that, once deployed, Envoyer sets up a /storage folder that maps to the Laravel structure one level below the /current directory and creates a symlink. When Envoyer pulls down the release, it deletes the storage directory from your repo. The reason for this is so that you can have one consistend location for things like logs or cached files/sessions AFTER you are up and running.
So, long story short, on Envoyer the linking of storage is a production convenience for your consistent storage needs. If you have data needed in a migration, you need to store it elsewhere.
Of course, this is explained perfectly starting around 1:55 here if you actually watch and listen: https://laracasts.com/series/envoyer/episodes/2