I might be missing something but it looks to me that there is a very simple solution to your problem. Rename the controller from "plugin_wiki" to "pretty_url". Then use the following routes.py:
routers = dict( app1 = dict( domain = "domain1.com", default_controller = "default", default_function = "myfunc1" ), app2 = dict( domain = "domain2.com", default_controller = "default", default_function = "myfunc2" ) )