F3 does not force/require you to use its template engine.
Having said that, you can certainly use templates stored in a database. However, you lose debugging capabilities because you have to use resolve() which uses eval() internally - which might not be in accordance with your development taste. Files are still the best way to go because of enhanced debugging and PHP's internal caching capabilities.
As far as performance is concerned, the only time benchmarking makes sense is during the template compilation, i.e. conversion to PHP code. That process though is a one-time activity. It doesn't matter then if one template engine is faster than the other by a few msecs.
All that on the table, F3 has three template engines for you to choose from. You can use Twig, Smarty, or whatever. After all, programming convenience and readability are the best reasons for choosing one over the other. Benchmarking template engines is for nitpickers.