It's important to understand that the typical reason that this scenario is done is because in classic three act story structure, the end of the second act is the hero at their lowest point, so to make the narrative and gameplay sides of the game cohesive, developers create a situation in which the player is also at their lowest point from gameplay ability standpoint as well.
Of course, it's all in the execution, and there's surely plenty of examples over the years of this type of thing being done poorly. As for recent examples where it's done well, I'll go with Ghost of Tsushima. The sequence is fairly short so it doesn't overstay it's welcome/get frustrating, it uses stealth mechanics that have already been developed throughout the game rather than newly introduce any stealth elements just for this section, and it allows you to listen in on the people around you and get a lot of narrative information while you're doing it. Plus it culminates in an extremely emotional moment to end the sequence.