Most of the time the added "extra stuff between the player and the big fight" are cinematics and dialogues because this is an story-driven game. A great example is the fight against Letho in Witcher 2, where you got a cinematic just before the fight so you had to drink potions a while back. Even if there are not cinematics or dialogues, there will probably be little fights before the "big one" and the effect of the potion won't be wasted.Cinematics aren't the whole problem, the problem is preparing before entering an area and being able to use the potions when you need them, allowing level designers to put some extra stuff between the player and the actual big fight they've prepared for, without having to worry about timer constraints. Cutscenes are only part of the issue.
I still stand by saying that the timer should just be stopped between cinematics or anything where the player has not a complete control over Geralt.