Site pages are customized pages and are saved in to content database. So when you use the SharePoint designer to make custom changes it saves the changes in to content database. If you want to make generic pages in a site collection which will be used by every one, like for instance the ‘Settings.aspx’ page then you need to use application pages.
In other words Site pages are nothing but customized pages stored in content, while application pages are generic pages which will be used by all the sites in a site collection.
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