I use shared installs with cpanel/fantastico, I found it much easier to use one of the many cpanel apis, which is ultimately http requests. But I would still like to know what the gurus think about then, ftp /sftp updates and the kind of organization as your question suggests.
I end up having a single wordpress install to update and symlink each site to this install ie: plugins, themes, custom stuff
I still have not managed sorting out the admin folder, but if my system is in a good mood, I can install in less than a minute with custom template, plugs etc, (pieace of cake for you guys,but auto-satisfaction does not hurt

)
the idea being I test locally, then upload once. and it can be done on multpile servers by keeping an update log
I suppose in boxed environment the situation would be different