At the moment, the site you get from using the 'koha' package doesn't integrate with the management system (based around koha-list) that koha-common provides. This means that things like zebra and other cron jobs don't work.
If the koha package installed its default site into the location that koha-common expects (/etc/koha/sites), then koha-common will be able to manage all these things pretty much automatically.
This is a pretty low-priority thing, but I would like to do it should I end up with the time and nothing else to do. So I'll leave it in this state for now.
The koha package is not used these days.