Setup fees depend strictly on the options selected when you order the server. Typically, the standard packages with modest configuration changes do not have any setup fees associated with them. When the configuration deviates significantly from the published plan there may be a setup fee. Most setup fees when charged usually involve Windows servers. All fees are presented up front during the ordering process. There are no hidden charges.
When ordering you should also pay attention to specials offered. Typically if there is a setup fee they are most likely waived as part of the current promotion.