I'd guess the reason the level layouts are not "realistic" is simply to offer better gameplay. Level layouts in modern games (even bland ones like CoD) don't make much sense either, but they're better at hiding it.
Modern games usually feel waaaaaaay less realistic to me because they fall right into the uncanny valley.
You'll have some photorealistic landscape, or some crazy fantasy landscape that looks real enough to touch.
And then the realism falls away because half of the simple doors in the village can't be operated by your character (even though he's strong enough to fight a 50-foot dragon with his bare hands) and there's a 2 foot high fence you can't jump over even though your character is a literal superhuman. And all the characters look "real" but move like slightly creepy photorealistic mannequins.
That always feels a lot less "real" to me than something like Doom that's just the right level of abstract.
The levels in Doom don't feel realistic (compared to any place that exists in reality) but they feel real in the sense that they are tangible, understandable, consistent environments.
If that means having less objects to interact with but I can interact with them all, then it feels like I have real control and consequence in the world.
Moving my laser gattling gun in Fallout 4 up onto a table feels immersive. Not being able to navigate a small rock barrier breaks that.
I imagine for me that it is easier to suspend my disbelief when the world feels real rather than when it looks real.
In all seriousness, though, complaining about gravity not being right when you're fighting demons and your health is a percentage number? Gravity is the least of the 'real-world' concerns. It's just a gameplay device like any other.
Has there ever been a hospital drama where the doctors are frantically running around saying things like "Quick! This man is down to 12% health and falling rapidly!"?
Doom isn't set on a space craft or (orbiting) space station. It's set on Phobos, one of Mars' moons. Given the likely terrain and challenges of building a base there, it's entirely conceivable the layout could be like that. As to the surreal look, well it felt good enough and immersive enough for me when I first played it back in 1994; especially late at night where it'd give me the willys.