I wouldn't begin to assert that those games are bad; just that their decision to mesh strong cohesive narrative with open world design ends up doing a disservice to both the narrative and the open world. That doesn't mean the game as a whole is bad.

I can pull Mass Effect (lets say ME2, as its oftentimes cited as the strongest entry in the trilogy) as a nearly inassailable example of this dichotomy games are faced with (and this post does have spoilers for ME2, though not horribly big ones)

One of the biggest issues with ME2 narrative structure is a direct consequence of the open world design; the ludonarrative dissonance of talking with a crew member, being told "the ship my dad died on just started broadcasting a distress signal, ten years later, Shepherd we gotta go check it out right now", then agreeing to check it out, then waiting ten quests or 10 real world hours to go check it out. The narrative introduces urgency; the open world gives the player the agency to ignore that urgency. It would be powerful if the game recognized this, and tweaked dialog to say something like "well I would have liked to check it out sooner, but this will have to do" once you finally get around to it, but it does not; instead, it leaves us with the ludonarrative dissonance of everyone pretending like this is priority #1, has always been priority #1, even though I just spent thirty minutes in the captain's cabin trying on some new armor.

Same game: You speak with Samara, she says something like "its so refreshing to work with a crew of friends again, and to help you with your mission." Not once did I take Samara on a mission; she says this dialog no matter how often you deploy on missions with her.

Same game: Grunt is complaining about having an insatiable need to kill stuff, and his loyalty mission is to get him checked out by the Krogans. At first, I was like; woah! I also never took Grunt on any missions, not even once; is this the game reacting to him being locked up in his room all day, creating dynamic content in response to my gameplay decisions? A true integration of open world and narrative, player decisions impacting the way the story progresses in a deep and meaningful way? It isn't. He'll do that even if he's by your side for every mission killing thousands of mercenaries.

Here's the gist of it: When games try to integrate an open world with strong narrative, it is possible to do it in a fantastic and meaningful way, where the open world actually supports and builds upon the narrative. Imagine if refusing to utilize squad mates led to their desertion, which led to more missions to win them back, or spending all day side-questing leads them to ask questions about what their mission really is and why they joined.

By and large, games fail to do this, because its VERY hard. Open world games are exponential multivariadic systems; the player has a thousand things they can do at any time, trying to account for every thousand of those things, write dialog lines, record voice-over, in twenty languages... its impossibly difficult. Games which go beyond competent in this regard (and Mass Effect is FAR BEYOND competent; its VERY good) should be held up as paragons of the artform, because they attempted to integrate the thing video games do best (open-ended interactivity) with a more traditional narrative structure. But that doesn't mean sacrifices weren't made, and ultimately for me it comes down to: Mass Effect is a FANTASTIC game... but its narrative isn't.