Database installed with Store Manager is a kind of temporary database. It can be used for various purposes one of most valuable of them is PHP MySQL bridge.
Working with local (Embedded) database is much faster than working with remote one. Local database and remote (website) database are not the same. However, you can use your local database to store your remote database inside it, make changes and then just synchronize your local and remote – make changes locally and then upload them to the website database using Bridge connection.