What are the pros/cons/alternatives to creating a number of identical content types to allow for divergence?
Initially my approach was going to be much like theirs, to have one publications content type, and a publication type vocabulary to categorize them. 


The problem with this approach is that you won't be able to use pathauto to give them different paths per type. Ex: You want the books type to be /books/title-goes-here and the cars type be /cars/title-goes-here 

If books and cars are the same content type then node author would have to manually type in the url alias.

Also, how do you plan on theming them? If each type needs to be themed differently, I don't know how you're going to pull that off since they are all the same content type.

I think making 16 different content types is the way to go. You can always re-use existing fields whenever you can. 




  I'm already seeing a little bit of difficulty in the ability to make
  dynamic templates that cover the entire set of publication types.


You could use the Panels module which allows you to theme all 16 content types differently or the same. With panels you won't have to deal with tpl (template) files.

Checkout this Panels Video Tutorial series