I am not entirely sure about this, but it seems like the end app created operates like some kind of its own sandbox, so everything needs to be packaged from within, that's why the author emphasized SQLite as the featured database for the tool, some of the ways I'd suggest would be
- Sticking out with the SQLite database
- if you still want to use MySQL (haven't tried but seems sensible)
- Use a remotely/publically accessible instance (over the internet/IP address)
- Package a MySQL binary with your app and inject it into the environment as the app runs
putenv('PATH=/path/to/your/mysql/binaries:' . getenv('PATH'));
NOTE: You'll want to have the putenv function allowed in your php configuration
Cheers