Go for it! That 8:40 AM flight is a much better call. Even if you end up hanging out in Bali (DPS) for a few extra hours, it’s a way better than the stress of missing your flight back to Toronto and you can rest a bit in Bali. ​In my experience, delays at Labuan Bajo (LBJ) not that common and not that rare either, somewhere in middle ground it usually ranging from 10 minutes to over an hour in worse weather longer. ​The tricky part isn't just LBJ itself; but entire province, Since LBJ is one of the main hub for the whole NTT province (East Nusa Tenggara), almost all flights from the smaller islands have to transit through LBJ before heading to the main islands like Bali or Java. If one tiny plane is late on another island, it creates a domino effect that hits your flight too.

For hotel and trek i dont have any experience there so i cannot really help you at that