The OneDrive folder and client is finally working, and working well. OneDrive launches and configures itself for the user. When a user launches a Published Desktop, there is no problem. The install goes into C:\Program Files (x86)\ as it always should have.

We've switched over to FSLogix profile and Office containers, as well as installed OneDrive with the /allusers switch. We're in the process of building out a new 'Virtual Apps' Deployment based on Win2016.