When a developer creates a theme to sell someplace like Themeforest he/she is building something without knowing exactly how it will be used in the end. The developer will try to accommodate a range of possibilities but will not be able to plan for every eventuality. It is nearly impossible to create a one size fits all solution.

When developing for a specific site one can come up with a plan that fully lays out content requirements, navigation, user experience, features, functions etc.

If the project is using a pre-made theme there will invariably be things in the plan that the theme doesn’t handle straight out of the box. So as Tim indicates, the project will require customizations. Sometimes these are simple sometimes they are more complicated.

I usually build custom themes for specific projects, but I’ve worked on some sites involving existing themes. For these I’ve added custom post types and taxonomies, custom fields, added additional template files, modified existing files, written plug-ins to over-ride things in the parent’s function.php file, etc. So this can turn out to be quite a bit of work.

Additionally one will need to add the content, install and configure plug-ins for backups, security, Google Analytics, SEO and other features. One should also submit the sitemap to Google Webmasters, test the site in various browsers and devices, etc.

If this is a new company or domain you may also need to configure email. Then you need to train the client on the care and feeding of their site.

So there is still a lot to do that will take up billable hours before all is said and done.