You misunderstand. It means that a single application should not use two or more copies of the SQLite library to open the same database file.

As a practical matter, you really have to work hard to get an application to use two different copies of SQLite at the same time - all the while avoiding symbol collisions on link. You can do it, but it takes some work. And then on top of that your application has to decide to open two or more connections to the same database file, using different copies of SQLite in each case.