your admin info (like password, username, etc.) is stored in the database, and there isn't a database distributed with WP. The "agents" of course have to have their own empty database, and the installation procedure creates the necessary tables in the database, and writes the initial password which is emailed to the person who installs it.
So that kind of stuff doesn't travel along with the files you're making, but the stuff you want (themes plugins and hacks to the core-code) will travel with the ZIP you create
So I think you're good, but I'd expect to spend more than a few minutes hacking the Dashboard (if you wish) and the Write Post page.
Not sure about your custom-fields needs... I think the custom fields are written to the database, which, again, does not travel with the installation. So your "agents" might have to re-create the custom field keys you want.