Dont get me wrong here, i would love it if the game would have timed events that would happen simultaneously ...
So one of my characters would help one group, but never managed to reach other in time ...
And another of my characters would go different route and have completely different experience for that reason.
It sounds awesome to me ...
The problem is i cant quite imagine how would they manage to do this (system-wise), without creating other paradoxes.

Therefore its just easier (and most likely even more practical) to see all encounters as separate one-act scenarios, where you were never meaned to return.

In case of Waukeen's Rest, it could have been handled quite easily. Trigger the event by seeing smoke rising from some point (perhaps even have companion point it out), then if you decide to rest rather than investigate and do the stuff related to the fire, you'd get a cutscene where the fire is largely under control, Florick is standing outside (having been rescued by the Flaming Fist mercenaries) and tells you of the situation with the Grand Duke.
It's certainly doable. Does it take some effort? Sure, but it would be worth it in my opinion.
The situation with the Zhent caravan survivors and the gnolls would be even easier. Ignore them for too long and have the gnolls slaughter them. You'd still be able to get the chest and it's contents, you'd still get the fight with the gnolls (only difference is that you wouldn't get the "send them into the cave to slaughter" in the dialogue with the flind), the only thing you wouldn't get is the password to get into Zhent hideout (which could happen anyway depending on the dialogue goes).
Having a chance for failure or to miss out on some things is a good thing in a RPG. Having to take on some encounters without being fully rested can be fun and lead to developing new strategies to cope with the situation. That, as well, is a good thing.
Point is, if it's not mechanically urgent, then as a designer you must not create a situation in-universe where it seems like it is: If the Rest will wait for us to arrive, then we absolutely must not be able to see it burning before we get there.
Correct
