Those are solely dependent on the applications and not the server they are contained on. An example would be like that of Deluge Web, it uses it's own location for the crt file. There could be a manual include within the .conf that may be able to point to a specific location, however, the problem arises with users preferences and where they store certificates. Thus we let the applications handle these items on their own and the user will need to configure these independently.
I am working on sorting our forwards and proxies that may be able to implement the use of the servers ssl without any additional configurations needed. This will also be a means to change from IP:port# to IP/application. At the moment there is no ETA as we currently have other items sitting in our development pipeline that are being worked on and tested.