Interesting question. You can add “Gam Zu LiTova” to your question. In other words, why even acknowledging “Gam zu LiTova” if it’s all for the good.
I wonder if the answer is that good and bad is, indeed, as we perceive it relating to our small world, but not necessarily from a long-term and certainly not from a global perspective.
For example, if someone leaves his phone at home and loses 30 minutes returning to get it, that is definitely “bad” since nobody likes to be hassled and lose time, etc.
But it could be that, as a result of this “bad” delay, something good would happen *later/ultimately*. Maybe not. Either way, we don’t usually know.
But at the time one is late/delayed, I think the most appropriate reaction is gam zu liTova, meaning it’s for the *ultimate* best (and be makir tov for that) even though it is still very annoying now.
Hakaras HaTov is always appropriate, even in this case, but it’s obviously different than if someone gives a well-received shiur, where there’s no doubt that’s a “good” thing, and one would be even more grateful to Hashem for that good.