I would say templates not intended to be served directly by the webserver are in a similar class to cgi scripts, and should be treated in a similar way.

For my work application we do indeed have multiple installations of the same application serving multiple virtual hosts. We have all the files needed for a virtual host residing under one directory hierarchy, but the docroot is just one of those:

web1% ls /www/www.somehostname.com
cgi-bin/  docs/  httpd.conf  lib/  logs/  template/
web1% 

Note that since different hosts may be running at different versions of the software, the perl modules are also installed locally (.../lib) rather than into any shared space.

The installer knows where each of these files should go and what permissions and ownership they should have, so we only have to get that right in one place.

Hugo