Modifying database directly is not the best approach, because various problems can occur. In order to get a better picture of the whole situation I would like to kindly ask you to share a bit more details about the differences that you have noticed.
By design all the information for some Sitefinity modules is stored in separate database tables. As an example I can give you Sitefinity Forms module - for every new form a separate table is created. This is only e brief example for a difference between a brand new project and project with added content.
Do you want to have your say in the Sitefinity development roadmap? Do you want to know when a feature you requested is added or when a bug fixed? Explore the Telerik Sitefinity CMS Ideas&Feedback Portal
and vote to affect the priority of the items