I think if I have gotten enough criteria down, it should be simple enough to say why some games that are close in structure to a Metroid-like, aren’t Metroid-likes.
various Legends of Zelda aren’t Metroid-likes despite having open, persistent, interconnected worlds, and a series of power-ups that upgrade or expand combat/mobility/interactive/logistic function. I would say for one that is because even when they’re not all that linear, and, to be clear, they usually are pretty linear, they don’t do nearly enough to obscure the connections between the points on the critical path. Your various Hyrules and Hyrule Fields and Oceans have plenty of secrets within them, sure, and traversal around them can change over time as you get more tools, but it’s not as if the confines of the map expand so much as they increase in density. There will always be a sense of the totality of the game world from the beginning, and traversal is often pleasant, but is not engaging so much as it is immersive and theatric. You can never really get a sense of feeling lost. At least not for long, anyway.
Furthemore the game’s narrative or interface will heavily suggest an intended order for the critical path, even when it can be done out of order, which kind of dispels the illusion of non-linearity (which is a different thing than sequence breaking even if they can overlap). You can tell me that you can do the 7 Dark World dungeons in Link to the Past in a variety of orders, but there is clearly no real reason to do so, it doesn’t make them any more compelling to have a tool you got from a dungeon later in the intended sequence, if for no other reason than the game isn’t going to make a habit of punishing people for doing things in the intended order. It also calls to mind something else that makes Zelda games not like Metroid-likes, in that the parts that do get you to navigate and pathfind, the dungeons, are self contained experiences with little to no cohesion or interconnection between each other, even if there is that within them or if you were to remove the game world in between them. This tends to lend better to the narrative structure of Zelda games, it’s not like there’s anything wrong with them.
Dark Souls might be closer to the definition of a Metroid-like given how there is non-linearity, pathfinding and navigation, a reluctance to direct player to connections between the critical path points, an interconnected and looping game world that you can totally get lost in, and some gating but also many ways to sneak around it. However, I don’t think it is a Metroid-like because it eschews the genre convention of expanding the player’s mobility/interactive capabilities in favor of abstracting traversal through areas with mostly either Keys of various kinds (Blue Key opens Blue Door) or surmountable by sequence breaking via raw skill to overcome combat challenges. I think this creates a very different kind of attitude toward exploration–the confines of the physical spaces you find yourself in are usually pretty clearly communicated, and finding hidden areas is more a question of being observant and poking open an illusory wall than having a particular skill to recontextualize the physical space with a new way you can interact with it. Running through Undead Burg when you’re so strong you don’t care about being hit 'cause you got the key to Lower Undead Burg is not the same as returning to the first area of Super Metroid once you’ve got Super Missles. Again, as much as Dark Souls clearly owes to Metroid-likes, this doesn’t make Dark Souls lesser but different.