I'm still using JSTorrent (https://chrome.google.com/webstore/detail/jstorrent/anhdpjpo...).
It's impossible to implement the BitTorrent protocol using a webapp, which means that once Chrome Apps are gone I'll have to revert to using a native client, which I don't trust one bit.
Webapp + native gateway also means that the torrent traffic ends up being suspended/throttled if the tab isn't foregrounded or if you close it, something you wouldn't have to deal with if the native gateway was just a native torrent client. Chrome Apps had a background privileged context that could keep running even if no tabs were open (though Google naturally discouraged this unless the app needed it), something you can't really get with a PWA currently (though Service Workers come close if you keep the tab open, I think? Maybe?)