While it is not really answering your question, I think such a setup is a bad habbit and will eventually fail if its the only solution (its a good foundation). Especially when packages on the server have different versions and probably different functionality.
Project specific dependencies are much better... and can support things like CI and if you want to go in the direction of DevOps.
As I am using a Shiny Server Pro as well I put my ideas up for discussion:
Probably I'm wrong though with my views as unfortunately no one really replied to my thread so far...