This is a very good question.
I preferred to bundle libtransmission to offer a plug'n play experience across all platforms.
Regarding all the criticism here, I believe PikaTorrent should primarily focus on new or average torrent users. Advanced users might either modify the settings file manually for now (though guessing the path is not ideal), or perhaps PikaTorrent should expose a textarea to edit transmission settings (though this approach might be risky for average users).
In the meantime, I plan to expose a lot more Transmission settings in the UI. Even for me, PikaTorrent is not mature enough to fulfill all my needs. However, with more features to come and potential feature requests from users on GitHub, it might become a suitable BitTorrent client for advanced users and server usages.