Personally, I like the semi-open design. I understand how it can be annoying, but the labyrinthine nature, backtracking to places that change, exploring weird nooks and crannies unlocked by mid-late-game abilities... it all fits very well with the theme of the game. The Oldest House is about the furthest thing from a linear place. It exists beyond time and physics. Why would everything be a straight shot? Why would anything about it make good, humanistic sense? It's a place with but a glimmer of actual human influence. The majority of the structure you see was not BUILT by people. It's a construct influenced by outer beings who wish to work with/use people. So it learns about them and tries to gear the space for them... but like, they're extra-dimensional beings. So everything is kind of uncanny and betrays your default thinking, leading you to wonder how beings controlling the house perceive the physical reality, if they can, or even care to comprehend human sensibilities. It's a collective so severed from the reality that we perceive that simply navigating the house is laughably insulting to human intuition... because the forces behind it have no concept of such a thing.
Human intuition in the Control universe is a funny thing, too. It also has the ability to subtly alter reality. The Oldest House is like a big ball of clay with many hands shaping it. And it looks and feels like it. Humans are sort of the key to creation for extra-dimensional beings in this universe. Things extrapolate from human minds and become real, physical aspects of the world. The right idea from the right person at the right time can literally augment all of reality, beyond what humans themselves can perceive. But in the process, these things are corrupted by beings more able to recognize and use the power from their positioning in a more metaphysical realm, while humans typically don't realize that their very minds are portals to other dimensions and their thoughts constantly influence pockets in the universe. It's something seemingly every unseen force in the universe converges on - human imagination. They are not ordered - they are amorphous and chaotic. Human imagination brings structure, synthesis of new things. The setting of the game is marked-up by outer beings attempting to leverage human minds to perform what they, as more nascent and nonlinear beings fundamentally cannot. Again, it makes more sense as a chaotic mess, a bad approximation of what human spaces are meant to be like, what functions they are tooled for and why.
I actually like the earlier versions of the game, when it was even more obtuse. The map had less detail, no elevation. You basically just had the shape of the area and some walls on it, with department names and arrows strewn about. So you had to navigate largely using the many signs across the building, use the color and architectural coding built into the worldspaces. What really gets me about that, is how well it works when you eschew the map and follow the signs from where you are, just stumbling into weirdness as you go, forgetting why you even went that way to begin with. You wind up progressing the game before you even realize where you're headed.
The thing about it for me is... there really ARE two stories being told... and honestly, the one with Jesse, Dylan, The FBC dealing with the hiss, is like a blip on the radar of a much bigger world story. The world story kinda doesn't sell without the convoluted, semi-open Metroidvania layout. It's part of a whole suite of things meant to convey the nature of that world, and a linear design directly contradicts that nature. The Oldest House is an ever shifting and expanding place, so it has halls that lead to nowhere, or just seem needlessly convoluted. It has entire forgotten wings, and rooms linking in ways nobody would ever wish to link them. Consider that it is also corrupted by an entity that explicitly wishes to turn all that exists... into them. It is reaching in and changing things to stymie your progress - making it harder for Jesse to get where she needs to in order to stop the takeover.
Not everything has to be portrayed directly, but I do think that in this case, getting lost is meant to be part of the experience. It's meant to make you feel at least a little alienated and frustrated, like it wasn't made for you. The Oldest House isn't made for you to navigate effectively, as it not only seems to have its own will, but is under the influence of cosmic wills. Generally speaking, it ACTIVELY ADOPTS the secrecy and obfuscation that defines how the FBC operated from the beginning. They wanted to hide, so the House and the Board shifted the house and the reality in it to help them hide better... so much so that they now can't find anything and most documents are borderline unreadable. The layout is purposeful. The FBC and the Board that controls it from the shadows are doing security by obscurity, down to the building itself. They went in step with the FBC becoming more secretive, and then the house becoming more secretive in response, until it grew into the weirdly locked-down mess Jesse finds, that nobody left in the organization can even put solid history to at that point. The FBC itself seems unable to change this on its own, with most people in the organization simply adapting to these ever-emerging new paradigms in secrecy as they arise.
Point is... there are many layers to why the building is how it is. Much of the environmental storytelling is simply gone the moment you remove the non-linear elements from the levels, or at the very least is largely oprhaned from active player experiences. The game is constantly pivoting off of that in order to let you have a chance to learn more about the world and its REAL key players. I really don't think it works to have so many things in the game tell you it's a confusing, extradimensional space, and then have the player go through linear, easy-to-follow levels.
It's just not an A-to-B game, or an A-to-B story. The things that seem linear tend to be illusions. The reality of The Oldest House is non-euclidean. I think you kind of have to be willing to revel in being lost, not knowing where you're going or what is going on. The map is how it is to intentionally obfuscate things about the world you are in - it is meant to be nonsensical to leave room for you to stop and infer. If you try to rush past it, mentally or in exploration, you will meet that frustration head on. The ethos of the protagonist hinges on her not knowing what she's plunging into and being completely out of her element. You experience that yourself, just navigating the game world itself.
Maybe not for everyone, but I do think that making it linear would've greatly weakened the presentation of the world, which is sort of the actual focus of everything. You can't really grasp the story without being immersed in the world itself. The point of the game is not to get to the final arc - it's more about taking the moments in. The game basically punishes you with frustration for trying to play it like a normal, linear game. It mirrors Jesse, who over time cares less about why she's even there and more comes to accept that there is no endpoint, and that reality itself is ever unfolding. And I believe the level design is directing you towards that. I mean, we are talking about a game where a dead end 10x10 room opens up to a sprawling hall with 200ft ceilings of crawling concrete, dancing like something out of an M.C. Escher sketch, seemingly unable to decide on its final geometric form, because a floating TV possessed by outer beings noticed the protagonist touching it... you know? Why in god's name would a building like that ever HOPE to make any sense?!